From 909954eb8be6e2b004044d39af629fd65e8bfafc Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Sun, 22 Sep 2024 19:33:13 +0000 Subject: [PATCH] Add changes --- data.js | 2632 ++++++++++++++++++++++++++-------------------------- skips.json | 360 +++---- 2 files changed, 1496 insertions(+), 1496 deletions(-) diff --git a/data.js b/data.js index 8bc3560..b4ae127 100644 --- a/data.js +++ b/data.js @@ -1,5 +1,491 @@ var data = [ + { + "config_readme": null, + "data_format": 2, + "description": "Snakemake workflow to analyse hematological malignancies in whole genome data", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/rules/cnvkit.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/rules/mutectcaller_to_tsv.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/rules/fix_af.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/rules/peddy_create_ped.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/rules/export.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/rules/dux4_rearrangements.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/rules/manta_to_tsv.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/rules/sample_order_multiqc.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/rules/gatk_cnv_denoise_read_counts_by_sex.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/rules/cnvkit_table.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/rules/html_output.smk\": Formatted content is different from original\n[INFO] 13 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "clinical-genomics-uppsala/fluffy_hematology_wgs", + "latest_release": "v1.1.0", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/Snakefile\", line 7, in \u003cmodule\u003e\n include: \"rules/common.smk\"\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/rules/common.smk\", line 12, in \u003cmodule\u003e\n from hydra_genetics.utils.resources import load_resources\n\nModuleNotFoundError: No module named \u0027hydra_genetics\u0027\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 0, + "subscribers_count": 2, + "topics": [], + "updated_at": 1723713011.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": null, + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp95qzm81x/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "MindTheGap-ERC/Triangle_workflow", + "latest_release": null, + "linting": "WorkflowError:\nNo storage provider found for query irods://nluu12p/home/research-test-christine/triangle/{param_file}.mat. Either install the required storage plugin or check your query. Also consider to explicitly specify the storage provider to get a more informative error message.\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 0, + "subscribers_count": 4, + "topics": [], + "updated_at": 1723661311.0 + }, + { + "config_readme": "\u003cp\u003eDescribe how to configure the workflow (using config.yaml and maybe additional files).\nAll of them need to be present with example entries inside of the config folder.\u003c/p\u003e\n", + "data_format": 2, + "description": null, + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmptaafhdwz/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "SveTho/bcl2fastq2_workflow", + "latest_release": null, + "linting": null, + "mandatory_flags": { + "desc": null, + "flags": null + }, + "report": true, + "software_stack_deployment": { + "conda": true, + "singularity": false, + "singularity+conda": false + }, + "standardized": true, + "stargazers_count": 0, + "subscribers_count": 1, + "topics": [], + "updated_at": 1723630209.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": "PacBio Jasmine pipeline, penalized regression, and DMR identification", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpup7dp332/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "aliciasillers/Preliminary-CpG-Data-Analysis", + "latest_release": null, + "linting": "Lints for rule pbmm2 (line 18, /tmp/tmpup7dp332/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule cpgtools (line 44, /tmp/tmpup7dp332/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 0, + "subscribers_count": 1, + "topics": [], + "updated_at": 1723591308.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": "Deep mutational scanning of the MERS-CoV and PDF-2180 receptor-binding domains", + "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmp2b6mul21/Snakefile\": TabError: inconsistent use of tabs and spaces in indentation (\u003cstring\u003e, line 351)\n[INFO] In file \"/tmp/tmp2b6mul21/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n\nsnakefmt version: 0.10.2", + "full_name": "tstarrlab/MERS-PDF2180-RBD_DMS", + "latest_release": null, + "linting": "TabError in file \u003cstring\u003e, line 351:\ninconsistent use of tabs and spaces in indentation:\n \tconfig[\u0027codon_variant_table_file_MERS_rpk\u0027],\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/tokenize.py\", line 580, in _generate_tokens_from_c_tokenizer\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/tokenize.py\", line 576, in _generate_tokens_from_c_tokenizer\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 0, + "subscribers_count": 0, + "topics": [], + "updated_at": 1723589726.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": "Benchmark for the AI LLM integration project", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpmumhq60x/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "xwiki-contrib/ai-llm-benchmark", + "latest_release": null, + "linting": "Lints for rule download (line 47, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule translate_to_french (line 64, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule translate_to_german (line 91, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule index (line 118, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule split (line 140, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param file is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule collect (line 167, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param input_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param file is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule eval_summary (line 202, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule eval_text_generation (line 234, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule eval_rag_qa (line 265, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule generate_plots (line 300, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule report (line 333, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule generate_model_outputs_report (line 370, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable PLOTS_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable EVALUATION_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule calculate_average_power (line 403, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule archive (line 431, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule clean (line 465, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable EVALUATION_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable TASKS_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable OUTPUT_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable SNAKEOUT_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable PLOTS_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable REPORTS_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable OUTPUT_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable PLOTS_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable RESULTS_SUMMARIZATION_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable RESULTS_TEXT_GENERATION_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable RESULTS_QA_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 0, + "subscribers_count": 47, + "topics": [], + "updated_at": 1723575430.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": "WIP HIBF benchmarks", + "formatting": null, + "full_name": "seqan/hibf_benchmarks", + "latest_release": null, + "linting": "Lints for rule plot_landingpage (line 42, /tmp/tmpjpma0sez/workflow/rules/plot.smk):\n * Param HTML_DIR is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 0, + "subscribers_count": 6, + "topics": [], + "updated_at": 1723547496.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": "Remove and Quantify Organism Spike Reads from Sequencing Data", + "formatting": "[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\|\u0027\n[DEBUG] In file \"/tmp/tmpkzm451zl/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "mskcc-microbiome/spikequant", + "latest_release": null, + "linting": "/tmp/tmpkzm451zl/workflow/Snakefile:689: SyntaxWarning: invalid escape sequence \u0027\\|\u0027\n/tmp/tmpkzm451zl/workflow/Snakefile:715: SyntaxWarning: invalid escape sequence \u0027\\|\u0027\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpkzm451zl/workflow/Snakefile\", line 19, in \u003cmodule\u003e\n #mapper = \"minimap2-sr\"\n ^^^^^^^^^^^^^^^^^\n\nAssertionError: spiketable is a required config argument!\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 0, + "subscribers_count": 1, + "topics": [], + "updated_at": 1723506913.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": null, + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp00x3u9xj/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp00x3u9xj/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp00x3u9xj/workflow/rules/reference.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp00x3u9xj/workflow/rules/recomb.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp00x3u9xj/workflow/rules/octomom.smk\": Formatted content is different from original\n[INFO] 5 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "A1um/mixed-experiment-workflow", + "latest_release": null, + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp00x3u9xj/workflow/Snakefile\", line 6, in \u003cmodule\u003e\n include: \"rules/recomb.smk\"\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp00x3u9xj/workflow/rules/common.smk\", line 9, in \u003cmodule\u003e\n samples = pd.read_json(config[\"sample_sheet\"], orient=\"records\") # noqa: F821\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/json/_json.py\", line 791, in read_json\n json_reader = JsonReader(\n ^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/json/_json.py\", line 904, in __init__\n data = self._get_data_from_filepath(filepath_or_buffer)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/json/_json.py\", line 960, in _get_data_from_filepath\n raise FileNotFoundError(f\"File {filepath_or_buffer} does not exist\")\n\nFileNotFoundError: File ./config/workflow.json does not exist\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 0, + "subscribers_count": 1, + "topics": [], + "updated_at": 1723498924.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": null, + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/04_left_trim.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/06_select_indel.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/13_snpEff.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/11_annovar_snp.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/00_fa_index.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/00_bam_index.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/12_annovar_ind.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/03_genotype_gvcf.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/10_bcftools_norm_ind.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/07_filter_snp.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/08_filter_indel.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/05_select_snp.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/02_combine_gvcf.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/00_picard_dict.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/09_bcftools_norm_snp.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/01_haplotype_caller.smk\": Formatted content is different from original\n[INFO] 17 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "DariaKIL/WES_Cardiomyopathy", + "latest_release": null, + "linting": "Lints for snakefile /tmp/tmpebsle3xl/Snakefile:\n * Absolute path \"/mnt/IMBG-NGS-Analysys/StudentsWork\" in line 8:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/reference\" in line 18:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/hs37d5\" in line 19:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/ExomesData/{sample}.bam\" in line 24:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/ExomesData/{sample}.bam.bai\" in line 31:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/{sample}.g.vcf.gz\" in line 32:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/combine.g.vcf.gz\" in line 33:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/combine_genotype.g.vcf.gz\" in line 34:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/left_trim_combine_genotype.g.vcf.gz\" in line 35:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/snp_left_trim_combine_genotype.g.vcf.gz\" in line 36:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/indel_left_trim_combine_genotype.g.vcf.gz\" in line 37:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/filter_snp_left_trim_combine_genotype.g.vcf.gz\" in line 38:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/filter_indel_left_trim_combine_genotype.g.vcf.gz\" in line 39:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/norm_filter_snp_left_trim_combine_genotype.vcf\" in line 40:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/norm_filter_indel_left_trim_combine_genotype.vcf\" in line 41:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/snp_myanno.hg19_multianno.vcf\" in line 42:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/indel_myanno.hg19_multianno.vcf\" in line 43:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/combine_genotype_snpEff.vcf\" in line 44:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/00_fa_index.smk\" in line 50:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/00_bam_index.smk\" in line 51:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/00_picard_dict.smk\" in line 52:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/01_haplotype_caller.smk\" in line 53:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/02_combine_gvcf.smk\" in line 54:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/03_genotype_gvcf.smk\" in line 55:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/04_left_trim.smk\" in line 56:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/05_select_snp.smk\" in line 57:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/06_select_indel.smk\" in line 58:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/07_filter_snp.smk\" in line 59:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/08_filter_indel.smk\" in line 60:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/09_bcftools_norm_snp.smk\" in line 61:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/10_bcftools_norm_ind.smk\" in line 62:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/11_annovar_snp.smk\" in line 63:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/12_annovar_ind.smk\" in line 64:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/13_snpEff.smk\" in line 65:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 18:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 24:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 29:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 32:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 33:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 34:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 35:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 36:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 37:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 38:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 39:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 40:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 41:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 42:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 43:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 44:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 50:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 51:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 52:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 53:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 54:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 55:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 56:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 57:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 58:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 59:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 60:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 61:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 62:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 63:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 64:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 65:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/00_fa_index.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for snakefile /tmp/tmpebsle3xl/rules/00_bam_index.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/ExomesData/{sample}.bam\" in line 4:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/ExomesData/{sample}.bam.bai\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 5:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/00_picard_dict.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for snakefile /tmp/tmpebsle3xl/rules/01_haplotype_caller.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/ExomesData/{sample}.bam\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/ExomesData/{sample}.bam.bai\" in line 6:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/{sample}.g.vcf.gz\" in line 10:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 6:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 7:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/02_combine_gvcf.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/{sample}.g.vcf.gz\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/combine.g.vcf.gz\" in line 7:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 7:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/03_genotype_gvcf.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/combine.g.vcf.gz\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/combine_genotype.g.vcf.gz\" in line 7:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 7:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/04_left_trim.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/combine_genotype.g.vcf.gz\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/left_trim_combine_genotype.g.vcf.gz\" in line 7:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 7:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/05_select_snp.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/left_trim_combine_genotype.g.vcf.gz\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/snp_left_trim_combine_genotype.g.vcf.gz\" in line 7:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 7:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/06_select_indel.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/left_trim_combine_genotype.g.vcf.gz\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/indel_left_trim_combine_genotype.g.vcf.gz\" in line 7:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 7:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/07_filter_snp.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/indel_left_trim_combine_genotype.g.vcf.gz\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/filter_snp_left_trim_combine_genotype.g.vcf.gz\" in line 7:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 7:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/08_filter_indel.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/indel_left_trim_combine_genotype.g.vcf.gz\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/filter_indel_left_trim_combine_genotype.g.vcf.gz\" in line 7:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 7:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/09_bcftools_norm_snp.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/filter_snp_left_trim_combine_genotype.g.vcf.gz\" in line 4:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/norm_filter_snp_left_trim_combine_genotype.vcf\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 5:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/10_bcftools_norm_ind.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/filter_indel_left_trim_combine_genotype.g.vcf.gz\" in line 4:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/norm_filter_indel_left_trim_combine_genotype.vcf\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 5:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/11_annovar_snp.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/norm_filter_snp_left_trim_combine_genotype.vcf\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/snp_myanno.hg19_multianno.vcf\" in line 7:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/snp_myanno\" in line 10:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 7:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 10:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/12_annovar_ind.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/norm_filter_indel_left_trim_combine_genotype.vcf\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/indel_myanno.hg19_multianno.vcf\" in line 7:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/indel_myanno\" in line 10:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 7:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 10:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/13_snpEff.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/combine_genotype.g.vcf.gz\" in line 4:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/combine_genotype_snpEff.vcf\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 5:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule fa_index (line 5, /tmp/tmpebsle3xl/rules/00_fa_index.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule bam_index (line 5, /tmp/tmpebsle3xl/rules/00_bam_index.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule picard_dict (line 5, /tmp/tmpebsle3xl/rules/00_picard_dict.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule haplotype_caller (line 5, /tmp/tmpebsle3xl/rules/01_haplotype_caller.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule combine_gvcf (line 5, /tmp/tmpebsle3xl/rules/02_combine_gvcf.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule genotype_gvcf (line 5, /tmp/tmpebsle3xl/rules/03_genotype_gvcf.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable ref from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule left_trim (line 5, /tmp/tmpebsle3xl/rules/04_left_trim.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule select_snp (line 5, /tmp/tmpebsle3xl/rules/05_select_snp.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule select_indel (line 5, /tmp/tmpebsle3xl/rules/06_select_indel.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule snp_filter (line 5, /tmp/tmpebsle3xl/rules/07_filter_snp.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule indel_filter (line 5, /tmp/tmpebsle3xl/rules/08_filter_indel.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule bcftools_norm_snp (line 5, /tmp/tmpebsle3xl/rules/09_bcftools_norm_snp.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule bcftools_norm_ind (line 5, /tmp/tmpebsle3xl/rules/10_bcftools_norm_ind.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule anovar_snp (line 5, /tmp/tmpebsle3xl/rules/11_annovar_snp.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param vcf is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule anovar_ind (line 5, /tmp/tmpebsle3xl/rules/12_annovar_ind.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param vcf is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule snpEff_snp (line 5, /tmp/tmpebsle3xl/rules/13_snpEff.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 0, + "subscribers_count": 1, + "topics": [], + "updated_at": 1723453165.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": null, + "formatting": null, + "full_name": "bjoernellens1/pypsa-eur-project", + "latest_release": null, + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmplwxdek0h/Snakefile\", line 13, in \u003cmodule\u003e\n from scripts._helpers import path_provider, copy_default_files, get_scenarios, get_rdir\n\n File \"/tmp/tmplwxdek0h/scripts/_helpers.py\", line 23, in \u003cmodule\u003e\n from tqdm import tqdm\n\nModuleNotFoundError: No module named \u0027tqdm\u0027\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 0, + "subscribers_count": 1, + "topics": [], + "updated_at": 1723384817.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": "Snakemake workflow to map PacBio HiFi reads back to an assembly and check for misassemblies at specific regions via NucFlag.", + "formatting": null, + "full_name": "logsdon-lab/Snakemake-NucFlag", + "latest_release": "v0.1.0", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmptyt7hvk6/logsdon-lab-Snakemake-NucFlag-9428dd5/workflow/Snakefile\", line 6, in \u003cmodule\u003e\n\n File \"/tmp/tmptyt7hvk6/logsdon-lab-Snakemake-NucFlag-9428dd5/workflow/rules/common.smk\", line 37, in get_sample_assemblies_and_reads\n for sm in config[\"samples\"]:\n ^^^^^^^^^^^^^^^^^^^\n\nKeyError: \u0027samples\u0027\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 0, + "subscribers_count": 0, + "topics": [], + "updated_at": 1723304315.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": "next step after recount-pump in the monorail pipeline", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpj8zjb2fc/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "langmead-lab/recount-unify", + "latest_release": null, + "linting": "need to pass values for \u0027gene_rejoin_mapping\u0027 and \u0027exon_rejoin_mapping\u0027 and \u0027sample_ids_file\u0027 and \u0027num_samples\u0027 for the initial rejoining part of the pipeline!\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 0, + "subscribers_count": 5, + "topics": [], + "updated_at": 1723235817.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": null, + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp22brxynr/rules/demand.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp22brxynr/rules/model.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp22brxynr/rules/wind-and-solar.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp22brxynr/rules/doc.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp22brxynr/rules/biofuels.smk\": Formatted content is different from original\n[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\/\u0027\n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\/\u0027\n[DEBUG] In file \"/tmp/tmp22brxynr/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp22brxynr/rules/transmission.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp22brxynr/rules/nuclear.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp22brxynr/rules/hydro.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp22brxynr/rules/shapes.smk\": Formatted content is different from original\n[INFO] 10 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "calliope-project/euro-calliope-modular", + "latest_release": null, + "linting": "Using workflow specific profile profiles/default for setting default command line arguments.\n/tmp/tmp22brxynr/Snakefile:50: SyntaxWarning: invalid escape sequence \u0027\\/\u0027\n \n/tmp/tmp22brxynr/Snakefile:114: SyntaxWarning: invalid escape sequence \u0027\\/\u0027\n \"techs/supply/open-field-solar-and-wind-onshore.yaml\",\nLints for snakefile /tmp/tmp22brxynr/Snakefile:\n * Absolute path \"/\" if config[\" in line 8:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 30:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 54:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 72:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 89:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 100:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmp22brxynr/./rules/biofuels.smk:\n * Path composition with \u0027+\u0027 in line 57:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmp22brxynr/./rules/model.smk:\n * Path composition with \u0027+\u0027 in line 4:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmp22brxynr/./rules/transmission.smk:\n * Path composition with \u0027+\u0027 in line 26:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 44:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule units (line 1, /tmp/tmp22brxynr/./rules/shapes.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule units_without_shape (line 29, /tmp/tmp22brxynr/./rules/shapes.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule download_potentials (line 9, /tmp/tmp22brxynr/./rules/wind-and-solar.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule potentials (line 40, /tmp/tmp22brxynr/./rules/wind-and-solar.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule download_capacity_factors_wind_and_solar (line 92, /tmp/tmp22brxynr/./rules/wind-and-solar.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule area_to_capacity_limits (line 123, /tmp/tmp22brxynr/./rules/wind-and-solar.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule capacity_factors_onshore_wind_and_solar (line 161, /tmp/tmp22brxynr/./rules/wind-and-solar.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule download_eez (line 210, /tmp/tmp22brxynr/./rules/wind-and-solar.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule eez (line 241, /tmp/tmp22brxynr/./rules/wind-and-solar.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule shared_coast (line 287, /tmp/tmp22brxynr/./rules/wind-and-solar.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule capacity_factors_offshore (line 326, /tmp/tmp22brxynr/./rules/wind-and-solar.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule download_biofuel_potentials_and_costs (line 3, /tmp/tmp22brxynr/./rules/biofuels.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule preprocess_biofuel_potentials_and_cost (line 34, /tmp/tmp22brxynr/./rules/biofuels.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule biofuels (line 73, /tmp/tmp22brxynr/./rules/biofuels.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule biofuel_tech_module (line 123, /tmp/tmp22brxynr/./rules/biofuels.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_units (line 17, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_download_hydro_generation_data (line 69, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_download_pumped_hydro_data (line 102, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_download_runoff_data (line 135, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_download_basins_database (line 172, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_download_stations_database (line 205, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_basins_database (line 238, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_stations_database (line 269, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_preprocess_basins (line 309, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_preprocess_hydro_stations (line 345, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_inflow_m3 (line 382, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_inflow_mwh (line 417, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_hydro_capacities (line 457, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_capacity_factors_hydro (line 488, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule data_hydro (line 100, /tmp/tmp22brxynr/./rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule download_raw_load (line 4, /tmp/tmp22brxynr/./rules/demand.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule electricity_load_national (line 35, /tmp/tmp22brxynr/./rules/demand.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule electricity_load (line 71, /tmp/tmp22brxynr/./rules/demand.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule jrc_power_plant_database_zipped (line 1, /tmp/tmp22brxynr/./rules/nuclear.smk):\n * Do not access input and output files individually by index in shell commands:\n When individual access to input or output files is needed (i.e., just\n writing \u0027{input}\u0027 is impossible), use names (\u0027{input.somename}\u0027) instead\n of index based access.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#rules\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule jrc_power_plant_database (line 32, /tmp/tmp22brxynr/./rules/nuclear.smk):\n * Do not access input and output files individually by index in shell commands:\n When individual access to input or output files is needed (i.e., just\n writing \u0027{input}\u0027 is impossible), use names (\u0027{input.somename}\u0027) instead\n of index based access.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#rules\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule nuclear_regional_capacity (line 60, /tmp/tmp22brxynr/./rules/nuclear.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule model_input_locations (line 1, /tmp/tmp22brxynr/./rules/model.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule download_entsoe_tyndp_zip (line 4, /tmp/tmp22brxynr/./rules/transmission.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule entsoe_tyndp_xlsx (line 35, /tmp/tmp22brxynr/./rules/transmission.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule transmission_entsoe_tyndp_tech_module (line 70, /tmp/tmp22brxynr/./rules/transmission.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule transmission_linked_neighbours_tech_module (line 110, /tmp/tmp22brxynr/./rules/transmission.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_with_location_specific_data (line 91, /tmp/tmp22brxynr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_without_location_specific_data (line 134, /tmp/tmp22brxynr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_without_specific_data (line 147, /tmp/tmp22brxynr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule auxiliary_files (line 180, /tmp/tmp22brxynr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule model (line 213, /tmp/tmp22brxynr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule dag (line 290, /tmp/tmp22brxynr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule clean (line 311, /tmp/tmp22brxynr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 0, + "subscribers_count": 3, + "topics": [], + "updated_at": 1723213764.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": "A Snakemake pipeline for copy number variant calling without normal tissue samples", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpzqunecdj/workflow/rules/mutect2.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpzqunecdj/workflow/rules/mask_ref.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpzqunecdj/workflow/rules/map_bowtie2.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpzqunecdj/workflow/rules/bcf.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpzqunecdj/workflow/rules/umi_mapping.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpzqunecdj/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpzqunecdj/workflow/rules/map_bwa.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpzqunecdj/workflow/rules/qc_map.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmpzqunecdj/workflow/rules/cnv_calling_with_true_pon.smk\": InvalidPython: Black error:\n```\nCannot parse: 54:0: \u003cline number missing in source\u003e\n```\n\n[DEBUG] In file \"/tmp/tmpzqunecdj/workflow/rules/cnv_calling_with_true_pon.smk\": \n[WARNING] In file \"/tmp/tmpzqunecdj/workflow/rules/cnvkit.smk\": Keyword \"shell\" at line 160 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmpzqunecdj/workflow/rules/cnvkit.smk\": Keyword \"params\" at line 316 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpzqunecdj/workflow/rules/cnvkit.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpzqunecdj/workflow/rules/purecn.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpzqunecdj/workflow/rules/stats.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpzqunecdj/workflow/rules/trimming_fastqc.smk\": Formatted content is different from original\n[INFO] 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] 12 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "pedricolino/cnakepit", + "latest_release": null, + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpzqunecdj/workflow/Snakefile\", line 30, in \u003cmodule\u003e\n samples = read_sample(config[\u0027data\u0027][\u0027samples_in_directory\u0027])\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1026, in read_csv\n return _read(filepath_or_buffer, kwds)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 620, in _read\n parser = TextFileReader(filepath_or_buffer, **kwds)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1620, in __init__\n self._engine = self._make_engine(f, self.engine)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1880, in _make_engine\n self.handles = get_handle(\n ^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/common.py\", line 873, in get_handle\n handle = open(\n ^^^^^\n\nFileNotFoundError: [Errno 2] No such file or directory: \u0027resources/data/sample_sheet.tsv\u0027\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 0, + "subscribers_count": 1, + "topics": [ + "bioinformatics", + "bwa", + "cna", + "cnv", + "cnvkit", + "conda", + "copynumbervariation", + "mutect2", + "panels", + "purecn", + "sequencing-data", + "snakemake", + "targeted-sequencing" + ], + "updated_at": 1723212951.0 + }, + { + "config_readme": "\u003cp\u003eDescribe how to configure the workflow (using config.yaml and maybe additional files).\nAll of them need to be present with example entries inside of the config folder.\u003c/p\u003e\n", + "data_format": 2, + "description": "Snakemake workflow to call denovo dna variants on a RIL population", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp9m5bzqwx/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "Bioinflows-Bioversity-CIAT/denovo-dna-variant-calling", + "latest_release": null, + "linting": null, + "mandatory_flags": { + "desc": null, + "flags": null + }, + "report": true, + "software_stack_deployment": { + "conda": true, + "singularity": false, + "singularity+conda": false + }, + "standardized": true, + "stargazers_count": 0, + "subscribers_count": 0, + "topics": [], + "updated_at": 1723209947.0 + }, + { + "config_readme": "\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eGeneral Configuration\u003c/h1\u003e\u003ca id=\"user-content-general-configuration\" class=\"anchor\" aria-label=\"Permalink: General Configuration\" href=\"#general-configuration\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eTo configure this workflow, modify \u003ccode\u003econfig/config.yaml\u003c/code\u003e according to your needs, following the explanations provided in the file.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eOutput folders\u003c/h2\u003e\u003ca id=\"user-content-output-folders\" class=\"anchor\" aria-label=\"Permalink: Output folders\" href=\"#output-folders\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eBy default, this workflow stores the files obtained, parsed and aggregated into three different folders (\u003ccode\u003edownloaded/\u003c/code\u003e, \u003ccode\u003eparsed/\u003c/code\u003e \u003ccode\u003eaggregated/\u003c/code\u003e) in the working directory. This behavior can be changed with the entries \u003ccode\u003edownloaded_mriot_dir:\u003c/code\u003e, \u003ccode\u003eparsed_mriot_dir:\u003c/code\u003e and \u003ccode\u003eaggregated_mriot_dir:\u003c/code\u003e.\u003c/p\u003e\n\u003cp\u003eFiles corresponding to a specific MRIOT will be stored in a subfolder of the corresponding name. For instance, Exiobase 3 (in ixi system) for year 1995 aggregated to 74 sectors will be stored under \u003ccode\u003eparsed/exiobase3_ixi/exiobase3_ixi_1995_74_sectors.pkl\u003c/code\u003e.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eSector aggregation files\u003c/h2\u003e\u003ca id=\"user-content-sector-aggregation-files\" class=\"anchor\" aria-label=\"Permalink: Sector aggregation files\" href=\"#sector-aggregation-files\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThe workflow looks for aggregation files in the \u003ccode\u003eaggregation_csv_dir:\u003c/code\u003e (\u003ccode\u003econfig/aggregation_files\u003c/code\u003e) by default.\u003c/p\u003e\n\u003cp\u003eSome existing aggregation are included in the repository, and new ones can be added. If you think an aggregation file you designed would be a valuable contribution, don\u0027t hesitate to pull-request it !\u003c/p\u003e\n\u003cp\u003eThe folder structure follows the same as for outputs, for instance, the file used to aggregate Exiobase 3 to 74 sectors is looked under \u003ccode\u003econfig/aggregation_files/exiobase3_ixi/exiobase3_ixi_74_sectors.csv\u003c/code\u003e\u003c/p\u003e\n\u003cp\u003eFiles should be in csv format, with a first column \u003ccode\u003esector\u003c/code\u003e with all the original sectors of the MRIOT, and \u003ccode\u003egroup\u003c/code\u003e and \u003ccode\u003ename\u003c/code\u003e columns with the new ID and names to map the original sectors too.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eCommon aggregation\u003c/h2\u003e\u003ca id=\"user-content-common-aggregation\" class=\"anchor\" aria-label=\"Permalink: Common aggregation\" href=\"#common-aggregation\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eAs an additional way to aggregate different MRIOTs into a common one, this workflow also embarks a \u003ccode\u003econfig/aggregation_files/sectors_common_aggreg.ods\u003c/code\u003e file for this purpose.\u003c/p\u003e\n\u003cp\u003eThe sheet \u003ccode\u003ecommon_aggreg\u003c/code\u003e of the file defines the sector to aggregate to via \u003ccode\u003egroup_id\u003c/code\u003e and \u003ccode\u003esector_name\u003c/code\u003e columns. The following sheets, \u003ccode\u003e\u0026lt;mriot_name\u0026gt;_to_common_aggreg\u003c/code\u003e, have \u003ccode\u003eoriginal sector\u003c/code\u003e, \u003ccode\u003eto_id\u003c/code\u003e and a \u003ccode\u003enew sector\u003c/code\u003e columns auto computed from \u003ccode\u003eto_id\u003c/code\u003e.\u003c/p\u003e\n\u003cp\u003eAsking the workflow to build \u003ccode\u003eaggregated/icio2021/icio2021_2003_common_aggreg.pkl\u003c/code\u003e, for instance, will aggregate \u003ccode\u003eicio2021_2003_full.pkl\u003c/code\u003e to the sectors defined in the sheet \u003ccode\u003ecommon_aggreg\u003c/code\u003e based on the correspondence in \u003ccode\u003eicio2021_to_common_aggreg\u003c/code\u003e.\u003c/p\u003e\n\u003cp\u003eDisclaimer: This work is still under progress and still requires to be streamlined.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eParameters aggregation\u003c/h2\u003e\u003ca id=\"user-content-parameters-aggregation\" class=\"anchor\" aria-label=\"Permalink: Parameters aggregation\" href=\"#parameters-aggregation\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThe workflow also allows to build sector parameters files for the \u003ccode\u003eBoARIO\u003c/code\u003e model.\nWe provide a \u003ccode\u003econfig/mriot_params/exiobase3_ixi_full_sectors.csv\u003c/code\u003e \"master\" file that contains values we used with the model and this MRIOT, and from which similar files can be obtained for the other MRIOT, using \u003ccode\u003econfig/aggregation_files/exiobase3_ixi/exiobase3_ixi_to_other_mrio_sectors.ods\u003c/code\u003e.\u003c/p\u003e\n", + "data_format": 2, + "description": "Pipelines to parse and aggregate MRIOT data for BoARIO", + "formatting": "[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpfciba8yw/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpfciba8yw/workflow/rules/mrio_treatments.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpfciba8yw/workflow/rules/sectors_config.smk\": Formatted content is different from original\n[INFO] 3 file(s) would be changed \ud83d\ude2c\n[INFO] 4 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", + "full_name": "spjuhel/BoARIO-MRIOT-Tools", + "latest_release": null, + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpfciba8yw/workflow/Snakefile\", line 6, in \u003cmodule\u003e\n from boario_tools.regex_patterns import (\n\nModuleNotFoundError: No module named \u0027boario_tools\u0027\n\n", + "mandatory_flags": { + "desc": null, + "flags": null + }, + "report": false, + "software_stack_deployment": { + "conda": true, + "singularity": false, + "singularity+conda": false + }, + "standardized": true, + "stargazers_count": 0, + "subscribers_count": 1, + "topics": [], + "updated_at": 1723205425.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": "Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s). ", + "formatting": null, + "full_name": "pmenzel/score-assemblies-MIT", + "latest_release": "v1.2", + "linting": null, + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 0, + "subscribers_count": 1, + "topics": [ + "bacterial-genome-analysis", + "bioinformatics-pipeline", + "nanopore-sequencing", + "snakemake" + ], + "updated_at": 1723619591.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": "Snakemake workflow for bacterial genome assembly + polishing for Oxford Nanopore (ONT) sequencing using multiple tools.", + "formatting": null, + "full_name": "pmenzel/ont-assembly-snake-MIT", + "latest_release": "v1.4", + "linting": "Lints for snakefile /tmp/tmp5o1hg4iz/pmenzel-ont-assembly-snake-MIT-69fcb11/Snakefile:\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n * Path composition with \u0027+\u0027 in line 54:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 58:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 6:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 28:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 54:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 56:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 58:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 63:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 67:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule filtlong (line 227, /tmp/tmp5o1hg4iz/pmenzel-ont-assembly-snake-MIT-69fcb11/Snakefile):\n * Shell command directly uses variable filtlong_min_read_length from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule filtlongMB (line 272, /tmp/tmp5o1hg4iz/pmenzel-ont-assembly-snake-MIT-69fcb11/Snakefile):\n * Shell command directly uses variable filtlong_min_read_length from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule filtlongPC (line 318, /tmp/tmp5o1hg4iz/pmenzel-ont-assembly-snake-MIT-69fcb11/Snakefile):\n * Shell command directly uses variable filtlong_min_read_length from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule filtlongMBql (line 363, /tmp/tmp5o1hg4iz/pmenzel-ont-assembly-snake-MIT-69fcb11/Snakefile):\n * Shell command directly uses variable filtlong_min_read_length from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule canu (line 918, /tmp/tmp5o1hg4iz/pmenzel-ont-assembly-snake-MIT-69fcb11/Snakefile):\n * Shell command directly uses variable target_genome_size from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 0, + "subscribers_count": 1, + "topics": [ + "bacterial-genome-analysis", + "bioinformatics", + "bioinformatics-pipeline", + "nanopore-sequencing", + "snakemake", + "snakemake-workflow" + ], + "updated_at": 1723619513.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": "A snakemake-based workflow for converting Illumina\u0027s bcl files to fastq files with the option of further downstream analysis (using FastQC, STAR+RSeQC, cutadapt) and encryption via gocryptfs", + "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmp690v5jwz/rules/pe_processing.smk\": Keyword \"input\" at line 135 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[ERROR] In file \"/tmp/tmp690v5jwz/rules/pe_processing.smk\": InvalidPython: Black error:\n```\nCannot parse: 143:4: log:\n```\n\n[DEBUG] In file \"/tmp/tmp690v5jwz/rules/pe_processing.smk\": \n[DEBUG] In file \"/tmp/tmp690v5jwz/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmp690v5jwz/rules/fastqProcessing.smk\": Keyword \"input\" at line 196 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmp690v5jwz/rules/fastqProcessing.smk\": Keyword \"input\" at line 226 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmp690v5jwz/rules/fastqProcessing.smk\": Keyword \"output\" at line 379 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmp690v5jwz/rules/fastqProcessing.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp690v5jwz/rules/bcl2fastq.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp690v5jwz/rules/qcShort.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmp690v5jwz/Snakefile\": InvalidPython: Black error:\n```\nCannot parse: 1:6: needs to be here for the snakemake workflow catalogue\n\n(Note reported line number may be incorrect, as snakefmt could not determine the true line number)\n```\n\n[DEBUG] In file \"/tmp/tmp690v5jwz/Snakefile\": \n[WARNING] In file \"/tmp/tmp690v5jwz/rules/convert2fastq.smk\": Keyword \"output\" at line 95 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmp690v5jwz/rules/convert2fastq.smk\": Keyword \"output\" at line 114 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[ERROR] In file \"/tmp/tmp690v5jwz/rules/convert2fastq.smk\": NoParametersError: L170: In input definition.\n[DEBUG] In file \"/tmp/tmp690v5jwz/rules/convert2fastq.smk\": \n[DEBUG] In file \"/tmp/tmp690v5jwz/rules/qc.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp690v5jwz/rules/qc_pe.smk\": Formatted content is different from original\n[INFO] 3 file(s) raised parsing errors \ud83e\udd15\n[INFO] 6 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "WestGermanGenomeCenter/bcl2fastq2_Pipeline", + "latest_release": null, + "linting": "SyntaxError in file /tmp/tmp690v5jwz/Snakefile, line 1:\ninvalid syntax:\nneeds to be here for the snakemake workflow catalogue\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 0, + "subscribers_count": 1, + "topics": [], + "updated_at": 1723118553.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": "Mapping of RNAseq reads to sequences obtained from CryoEM in Toxoplasma gondii", + "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmpdpo1e4ok/Snakefile\": Keyword \"input\" at line 362 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpdpo1e4ok/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "glaParaBio/cryoem-mitoribosome-rnaseq", + "latest_release": null, + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpdpo1e4ok/Snakefile\", line 7, in \u003cmodule\u003e\n TGMITO = os.path.basename(config[\u0027tgmito\u0027])\n ^^^^^^^^^^^^\n\nKeyError: \u0027tgmito\u0027\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 0, + "subscribers_count": 1, + "topics": [], + "updated_at": 1723114523.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": "Multiplex Accurate Sensitive Quantitation (MASQ) analysis and primer design", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp_kkyaebk/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "amoffitt/MASQ", + "latest_release": null, + "linting": "Lints for snakefile /tmp/tmp_kkyaebk/Snakefile:\n * Absolute path \"/r1.fastq.gz\" in line 143:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/r2.fastq.gz\" in line 144:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/r1.fastq.gz\" in line 176:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/r2.fastq.gz\" in line 177:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/extended_var_table.txt\" in line 178:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/extended_var_table.txt\" in line 223:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 65:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 178:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 223:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 72:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 110:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 425:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 426:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule convert_SNV_table (line 122, /tmp/tmp_kkyaebk/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule barcode_split (line 150, /tmp/tmp_kkyaebk/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param output_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule fastqc (line 184, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule check_loci_extend_and_plot (line 219, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule sort_data_by_tag_and_locus (line 255, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule all_base_report (line 310, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule combine_within_tag_errors (line 361, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule tag_count_graphs_per_region (line 390, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule tag_count_graphs_combined (line 426, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule rollup_tags (line 461, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule combine_reports_alignment (line 501, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule combine_reports_basecount (line 530, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule combine_reports_per_base (line 558, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule combine_reports_rollup (line 586, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule combine_reports_readspertag (line 614, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule extract_variant_bases_from_report (line 643, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule plot_rollup_results (line 671, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule final_report (line 704, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule bad_loci (line 735, /tmp/tmp_kkyaebk/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule qc_plots (line 749, /tmp/tmp_kkyaebk/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n\nLints for rule filter_base_report (line 776, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 0, + "subscribers_count": 1, + "topics": [], + "updated_at": 1723065291.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": "Significantly improved bam2bakR implementation", + "formatting": null, + "full_name": "isaacvock/fastq2EZbakR", + "latest_release": null, + "linting": null, + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 0, + "subscribers_count": 1, + "topics": [], + "updated_at": 1723042307.0 + }, + { + "config_readme": "\u003cp\u003eThis pipeline requires two configuration file:\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003e\u003ccode\u003econfig.yaml\u003c/code\u003e\u003c/h1\u003e\u003ca id=\"user-content-configyaml\" class=\"anchor\" aria-label=\"Permalink: config.yaml\" href=\"#configyaml\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eA standard \u003ccode\u003eSnakemake\u003c/code\u003e configuration, yaml-formatted file containing a list of\nall parameters accepted in this workflow:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003esamples\u003c/code\u003e: Path to the file containing link between samples and their fastq file(s)\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003eparams\u003c/code\u003e: Per-tool list of optional parameters\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eExample:\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003esamples: config/samples.csv\n\n# Optional parameters\nparams:\n fair_bowtie2_mapping:\n bowtie2:\n # Optional parameters for bowtie2-build\n build: \"\"\n # Optional parameters for bowtie2-align\n align: \"\"\n sambamba:\n # Optional parameters for sambamba view\n view: \"--format \u0027bam\u0027 --filter \u0027mapping_quality \u0026gt;= 30 and not (unmapped or mate_is_unmapped)\u0027 \"\n # Optional parameters for sambamba markdup\n markdup: \"--remove-duplicates\"\n picard:\n # Mapping QC optional parameters\n metrics: \"\"\n\u003c/code\u003e\u003c/pre\u003e\n\u003cp\u003eA complete list of accepted keys is available \u003ca href=\"https://github.com/tdayris/fair_bowtie2_mapping/blob/main/workflow/schemas/config.schema.yaml\"\u003ein schemas\u003c/a\u003e,\nwith their default value, expected type, and human readable description.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003e\u003ccode\u003esamples.csv\u003c/code\u003e\u003c/h1\u003e\u003ca id=\"user-content-samplescsv\" class=\"anchor\" aria-label=\"Permalink: samples.csv\" href=\"#samplescsv\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eA CSV-formatted text file containing the following mandatory columns:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003esample_id\u003c/code\u003e: Unique name of the sample\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003eupstream_file\u003c/code\u003e: Path to upstream fastq file\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003especies\u003c/code\u003e: The species name, according to Ensembl standards\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003ebuild\u003c/code\u003e: The corresponding genome build, according to Ensembl standards\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003erelease\u003c/code\u003e: The corresponding genome release, according to Ensembl standards\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003edownstream_file\u003c/code\u003e: Optional path to downstream fastq file\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eExample:\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003esample_id,upstream_file,downstream_file,species,build,release\nsac_a,data/reads/a.scerevisiae.1.fq,data/reads/a.scerevisiae.2.fq,saccharomyces_cerevisiae,R64-1-1,110\n\u003c/code\u003e\u003c/pre\u003e\n\u003cp\u003eA complete list of accepted keys is available \u003ca href=\"https://github.com/tdayris/fair_bowtie2_mapping/blob/main/workflow/schemas/samples.schema.yaml\"\u003ein schemas\u003c/a\u003e,\nwith their default value, expected type, and human readable description.\u003c/p\u003e\n\u003cp\u003eWhile \u003ccode\u003eCSV\u003c/code\u003e format is tested and recommended, this workflow uses python\n\u003ccode\u003ecsv.Sniffer()\u003c/code\u003e to detect column separator. Tabulation and semicolumn are\nalso accepted as field separator. Remember that only comma-separator is\ntested.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003e\u003ccode\u003egenomes.csv\u003c/code\u003e\u003c/h1\u003e\u003ca id=\"user-content-genomescsv\" class=\"anchor\" aria-label=\"Permalink: genomes.csv\" href=\"#genomescsv\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThis file is fully optional. When missing, the genome sequences\nwill be downloaded from Ensembl and indexed.\u003c/p\u003e\n\u003cp\u003eA CSV-formatted text file containing the following mandatory columns:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003especies\u003c/code\u003e: The species name, according to Ensembl standards\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003ebuild\u003c/code\u003e: The corresponding genome build, according to Ensembl standards\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003erelease\u003c/code\u003e: The corresponding genome release, according to Ensembl standards\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eThe following columns are optional and are used to avoid downloading genomes:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003efasta\u003c/code\u003e: Path to the reference genome sequence (FASTA formatted)\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003efasta_index\u003c/code\u003e: Path to the reference genome sequence index (FAI formatted)\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003ebowtie2_dna_index\u003c/code\u003e: Path to the main directory containing reference index\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eExample:\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003especies,build,release,fasta,fasta_index,bowtie2_index\nhomo_sapiens,GRCh38,110,/path/to/sequence.fasta,/path/to/sequence.fasta.fai,/path/to/bowtie2_sequence/\nmus_musculus,GRCm38,99,,,\nmus_musculus,GRCm39,110,,,\n\u003c/code\u003e\u003c/pre\u003e\n\u003cp\u003eA complete list of accepted keys is available \u003ca href=\"https://github.com/tdayris/fair_bowtie2_mapping/blob/main/workflow/schemas/genomes.schema.yaml\"\u003ein schemas\u003c/a\u003e,\nwith their default value, expected type, and human readable description.\u003c/p\u003e\n\u003cp\u003eWhile \u003ccode\u003eCSV\u003c/code\u003e format is tested and recommended, this workflow uses python\n\u003ccode\u003ecsv.Sniffer()\u003c/code\u003e to detect column separator. Tabulation and semicolumn are\nalso accepted as field separator. Remember that only comma-separator is\ntested.\u003c/p\u003e\n", + "data_format": 2, + "description": "Align reads over a reference genome, filter aligned-reads, and mark duplicates", + "formatting": null, + "full_name": "tdayris/fair_bowtie2_mapping", + "latest_release": "4.2.0", + "linting": null, + "mandatory_flags": { + "desc": "Align ungapped reads to the genome with Bowtie2", + "flags": null + }, + "report": true, + "software_stack_deployment": { + "conda": true, + "singularity": false, + "singularity+conda": true + }, + "standardized": true, + "stargazers_count": 0, + "subscribers_count": 1, + "topics": [ + "bowtie2", + "multiqc", + "sambamba", + "snakemake", + "snakemake-workflow", + "snakemake-wrappers" + ], + "updated_at": 1723031584.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": null, + "formatting": "[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\d\u0027\n[DEBUG] In file \"/tmp/tmp8pqah41f/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "jorgenriseth/gMRI2FEM", + "latest_release": null, + "linting": "/tmp/tmp8pqah41f/Snakefile:32: SyntaxWarning: invalid escape sequence \u0027\\d\u0027\n SUBJECTS=config[\"subjects\"]\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp8pqah41f/Snakefile\", line 14, in \u003cmodule\u003e\n + \"conda activate $CONDA_ENV_NAME \u0026\u0026 \"\n ^^^^^^^^^^^^^^^^^^^^^^^^^^\n\nAttributeError: \u0027Workflow\u0027 object has no attribute \u0027use_singularity\u0027\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 0, + "subscribers_count": 1, + "topics": [], + "updated_at": 1723028673.0 + }, { "config_readme": "\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eConfiguration\u003c/h1\u003e\u003ca id=\"user-content-configuration\" class=\"anchor\" aria-label=\"Permalink: Configuration\" href=\"#configuration\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eWorkflow config\u003c/h2\u003e\u003ca id=\"user-content-workflow-config\" class=\"anchor\" aria-label=\"Permalink: Workflow config\" href=\"#workflow-config\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThe workflow requires configuration by modification of \u003ccode\u003econfig/config.yaml\u003c/code\u003e.\nFollow the explanations provided as comments in the file.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eSample \u0026amp; unit config\u003c/h2\u003e\u003ca id=\"user-content-sample--unit-config\" class=\"anchor\" aria-label=\"Permalink: Sample \u0026amp; unit config\" href=\"#sample--unit-config\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThe configuration of samples and units is specified as tab-separated value (\u003ccode\u003e.tsv\u003c/code\u003e) files.\nEach \u003ccode\u003e.tsv\u003c/code\u003e requires specific columns (see below), but extra columns may be present (however, will not be used).\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003e\u003ccode\u003esamples.tsv\u003c/code\u003e\u003c/h3\u003e\u003ca id=\"user-content-samplestsv\" class=\"anchor\" aria-label=\"Permalink: samples.tsv\" href=\"#samplestsv\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThe default path for the sample sheet is \u003ccode\u003econfig/samples.tsv\u003c/code\u003e.\nThis may be changed via configuration in \u003ccode\u003econfig/config.yaml\u003c/code\u003e.\u003c/p\u003e\n\u003cp\u003e\u003ccode\u003esamples.tsv\u003c/code\u003e requires only one column named \u003ccode\u003esample\u003c/code\u003e, which contains the desired names of the samples.\nSample names must be unique, corresponding to a physical sample.\nBiological and technical replicates should be specified as separate samples.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003e\u003ccode\u003eunits.tsv\u003c/code\u003e\u003c/h3\u003e\u003ca id=\"user-content-unitstsv\" class=\"anchor\" aria-label=\"Permalink: units.tsv\" href=\"#unitstsv\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThe default path for the unit sheet is \u003ccode\u003econfig/units.tsv\u003c/code\u003e.\nThis may be changed via configuration in \u003ccode\u003econfig/config.yaml\u003c/code\u003e.\u003c/p\u003e\n\u003cp\u003e\u003ccode\u003eunits.tsv\u003c/code\u003e requires four columns, named \u003ccode\u003esample\u003c/code\u003e, \u003ccode\u003eunit\u003c/code\u003e, \u003ccode\u003efq1\u003c/code\u003e and \u003ccode\u003efq2\u003c/code\u003e.\nEach row of the units sheet corresponds to a single sequencing unit.\nTherefore, for each sample specified in \u003ccode\u003esamples.tsv\u003c/code\u003e, one or more sequencing units should be present.\n\u003ccode\u003eunit\u003c/code\u003e values must be unique within each sample.\nA common example of an experiment with multiple sequencing units is a sample split across several runs/lanes.\u003c/p\u003e\n\u003cp\u003eFor each unit, the respective path to \u003ccode\u003eFASTQ\u003c/code\u003e files must be specified in the \u003ccode\u003efq1\u003c/code\u003e and \u003ccode\u003efq2\u003c/code\u003e columns.\nBoth columns must exist, however, the \u003ccode\u003efq2\u003c/code\u003e column may be left empty in the case of single-end sequencing experiments.\nThis is how one specifies whether single- or paired-end rules are run by the workflow.\u003c/p\u003e\n", "data_format": 2, @@ -4271,475 +4757,6 @@ var data = "topics": [], "updated_at": 1721945847.0 }, - { - "config_readme": null, - "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp95qzm81x/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "MindTheGap-ERC/Triangle_workflow", - "latest_release": null, - "linting": "WorkflowError:\nNo storage provider found for query irods://nluu12p/home/research-test-christine/triangle/{param_file}.mat. Either install the required storage plugin or check your query. Also consider to explicitly specify the storage provider to get a more informative error message.\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 0, - "subscribers_count": 4, - "topics": [], - "updated_at": 1723661311.0 - }, - { - "config_readme": "\u003cp\u003eDescribe how to configure the workflow (using config.yaml and maybe additional files).\nAll of them need to be present with example entries inside of the config folder.\u003c/p\u003e\n", - "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmptaafhdwz/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "SveTho/bcl2fastq2_workflow", - "latest_release": null, - "linting": null, - "mandatory_flags": { - "desc": null, - "flags": null - }, - "report": true, - "software_stack_deployment": { - "conda": true, - "singularity": false, - "singularity+conda": false - }, - "standardized": true, - "stargazers_count": 0, - "subscribers_count": 1, - "topics": [], - "updated_at": 1723630209.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": "PacBio Jasmine pipeline, penalized regression, and DMR identification", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpup7dp332/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "aliciasillers/Preliminary-CpG-Data-Analysis", - "latest_release": null, - "linting": "Lints for rule pbmm2 (line 18, /tmp/tmpup7dp332/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule cpgtools (line 44, /tmp/tmpup7dp332/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 0, - "subscribers_count": 1, - "topics": [], - "updated_at": 1723591308.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": "Deep mutational scanning of the MERS-CoV and PDF-2180 receptor-binding domains", - "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmp2b6mul21/Snakefile\": TabError: inconsistent use of tabs and spaces in indentation (\u003cstring\u003e, line 351)\n[INFO] In file \"/tmp/tmp2b6mul21/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n\nsnakefmt version: 0.10.2", - "full_name": "tstarrlab/MERS-PDF2180-RBD_DMS", - "latest_release": null, - "linting": "TabError in file \u003cstring\u003e, line 351:\ninconsistent use of tabs and spaces in indentation:\n \tconfig[\u0027codon_variant_table_file_MERS_rpk\u0027],\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/tokenize.py\", line 580, in _generate_tokens_from_c_tokenizer\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/tokenize.py\", line 576, in _generate_tokens_from_c_tokenizer\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 0, - "subscribers_count": 0, - "topics": [], - "updated_at": 1723589726.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": "Benchmark for the AI LLM integration project", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpmumhq60x/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "xwiki-contrib/ai-llm-benchmark", - "latest_release": null, - "linting": "Lints for rule download (line 47, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule translate_to_french (line 64, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule translate_to_german (line 91, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule index (line 118, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule split (line 140, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param file is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule collect (line 167, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param input_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param file is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule eval_summary (line 202, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule eval_text_generation (line 234, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule eval_rag_qa (line 265, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule generate_plots (line 300, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule report (line 333, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule generate_model_outputs_report (line 370, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable PLOTS_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable EVALUATION_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule calculate_average_power (line 403, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule archive (line 431, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule clean (line 465, /tmp/tmpmumhq60x/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable EVALUATION_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable TASKS_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable OUTPUT_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable SNAKEOUT_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable PLOTS_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable REPORTS_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable OUTPUT_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable PLOTS_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable RESULTS_SUMMARIZATION_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable RESULTS_TEXT_GENERATION_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable RESULTS_QA_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 0, - "subscribers_count": 47, - "topics": [], - "updated_at": 1723575430.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": "WIP HIBF benchmarks", - "formatting": null, - "full_name": "seqan/hibf_benchmarks", - "latest_release": null, - "linting": "Lints for rule plot_landingpage (line 42, /tmp/tmpjpma0sez/workflow/rules/plot.smk):\n * Param HTML_DIR is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 0, - "subscribers_count": 6, - "topics": [], - "updated_at": 1723547496.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": "Remove and Quantify Organism Spike Reads from Sequencing Data", - "formatting": "[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\|\u0027\n[DEBUG] In file \"/tmp/tmpkzm451zl/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "mskcc-microbiome/spikequant", - "latest_release": null, - "linting": "/tmp/tmpkzm451zl/workflow/Snakefile:689: SyntaxWarning: invalid escape sequence \u0027\\|\u0027\n/tmp/tmpkzm451zl/workflow/Snakefile:715: SyntaxWarning: invalid escape sequence \u0027\\|\u0027\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpkzm451zl/workflow/Snakefile\", line 19, in \u003cmodule\u003e\n #mapper = \"minimap2-sr\"\n ^^^^^^^^^^^^^^^^^\n\nAssertionError: spiketable is a required config argument!\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 0, - "subscribers_count": 1, - "topics": [], - "updated_at": 1723506913.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp00x3u9xj/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp00x3u9xj/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp00x3u9xj/workflow/rules/reference.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp00x3u9xj/workflow/rules/recomb.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp00x3u9xj/workflow/rules/octomom.smk\": Formatted content is different from original\n[INFO] 5 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "A1um/mixed-experiment-workflow", - "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp00x3u9xj/workflow/Snakefile\", line 6, in \u003cmodule\u003e\n include: \"rules/recomb.smk\"\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp00x3u9xj/workflow/rules/common.smk\", line 9, in \u003cmodule\u003e\n samples = pd.read_json(config[\"sample_sheet\"], orient=\"records\") # noqa: F821\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/json/_json.py\", line 791, in read_json\n json_reader = JsonReader(\n ^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/json/_json.py\", line 904, in __init__\n data = self._get_data_from_filepath(filepath_or_buffer)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/json/_json.py\", line 960, in _get_data_from_filepath\n raise FileNotFoundError(f\"File {filepath_or_buffer} does not exist\")\n\nFileNotFoundError: File ./config/workflow.json does not exist\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 0, - "subscribers_count": 1, - "topics": [], - "updated_at": 1723498924.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/04_left_trim.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/06_select_indel.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/13_snpEff.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/11_annovar_snp.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/00_fa_index.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/00_bam_index.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/12_annovar_ind.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/03_genotype_gvcf.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/10_bcftools_norm_ind.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/07_filter_snp.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/08_filter_indel.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/05_select_snp.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/02_combine_gvcf.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/00_picard_dict.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/09_bcftools_norm_snp.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpebsle3xl/rules/01_haplotype_caller.smk\": Formatted content is different from original\n[INFO] 17 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "DariaKIL/WES_Cardiomyopathy", - "latest_release": null, - "linting": "Lints for snakefile /tmp/tmpebsle3xl/Snakefile:\n * Absolute path \"/mnt/IMBG-NGS-Analysys/StudentsWork\" in line 8:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/reference\" in line 18:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/hs37d5\" in line 19:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/ExomesData/{sample}.bam\" in line 24:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/ExomesData/{sample}.bam.bai\" in line 31:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/{sample}.g.vcf.gz\" in line 32:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/combine.g.vcf.gz\" in line 33:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/combine_genotype.g.vcf.gz\" in line 34:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/left_trim_combine_genotype.g.vcf.gz\" in line 35:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/snp_left_trim_combine_genotype.g.vcf.gz\" in line 36:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/indel_left_trim_combine_genotype.g.vcf.gz\" in line 37:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/filter_snp_left_trim_combine_genotype.g.vcf.gz\" in line 38:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/filter_indel_left_trim_combine_genotype.g.vcf.gz\" in line 39:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/norm_filter_snp_left_trim_combine_genotype.vcf\" in line 40:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/norm_filter_indel_left_trim_combine_genotype.vcf\" in line 41:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/snp_myanno.hg19_multianno.vcf\" in line 42:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/indel_myanno.hg19_multianno.vcf\" in line 43:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/combine_genotype_snpEff.vcf\" in line 44:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/00_fa_index.smk\" in line 50:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/00_bam_index.smk\" in line 51:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/00_picard_dict.smk\" in line 52:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/01_haplotype_caller.smk\" in line 53:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/02_combine_gvcf.smk\" in line 54:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/03_genotype_gvcf.smk\" in line 55:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/04_left_trim.smk\" in line 56:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/05_select_snp.smk\" in line 57:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/06_select_indel.smk\" in line 58:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/07_filter_snp.smk\" in line 59:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/08_filter_indel.smk\" in line 60:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/09_bcftools_norm_snp.smk\" in line 61:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/10_bcftools_norm_ind.smk\" in line 62:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/11_annovar_snp.smk\" in line 63:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/12_annovar_ind.smk\" in line 64:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/rules/13_snpEff.smk\" in line 65:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 18:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 24:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 29:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 32:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 33:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 34:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 35:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 36:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 37:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 38:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 39:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 40:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 41:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 42:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 43:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 44:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 50:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 51:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 52:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 53:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 54:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 55:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 56:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 57:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 58:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 59:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 60:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 61:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 62:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 63:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 64:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 65:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/00_fa_index.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for snakefile /tmp/tmpebsle3xl/rules/00_bam_index.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/ExomesData/{sample}.bam\" in line 4:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/ExomesData/{sample}.bam.bai\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 5:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/00_picard_dict.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n\nLints for snakefile /tmp/tmpebsle3xl/rules/01_haplotype_caller.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/ExomesData/{sample}.bam\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/ExomesData/{sample}.bam.bai\" in line 6:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/{sample}.g.vcf.gz\" in line 10:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 6:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 7:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/02_combine_gvcf.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/{sample}.g.vcf.gz\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/combine.g.vcf.gz\" in line 7:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 7:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/03_genotype_gvcf.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/combine.g.vcf.gz\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/combine_genotype.g.vcf.gz\" in line 7:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 7:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/04_left_trim.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/combine_genotype.g.vcf.gz\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/left_trim_combine_genotype.g.vcf.gz\" in line 7:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 7:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/05_select_snp.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/left_trim_combine_genotype.g.vcf.gz\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/snp_left_trim_combine_genotype.g.vcf.gz\" in line 7:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 7:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/06_select_indel.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/left_trim_combine_genotype.g.vcf.gz\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/indel_left_trim_combine_genotype.g.vcf.gz\" in line 7:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 7:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/07_filter_snp.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/indel_left_trim_combine_genotype.g.vcf.gz\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/filter_snp_left_trim_combine_genotype.g.vcf.gz\" in line 7:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 7:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/08_filter_indel.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/indel_left_trim_combine_genotype.g.vcf.gz\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/filter_indel_left_trim_combine_genotype.g.vcf.gz\" in line 7:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 7:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/09_bcftools_norm_snp.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/filter_snp_left_trim_combine_genotype.g.vcf.gz\" in line 4:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/norm_filter_snp_left_trim_combine_genotype.vcf\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 5:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/10_bcftools_norm_ind.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/filter_indel_left_trim_combine_genotype.g.vcf.gz\" in line 4:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/norm_filter_indel_left_trim_combine_genotype.vcf\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 5:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/11_annovar_snp.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/norm_filter_snp_left_trim_combine_genotype.vcf\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/snp_myanno.hg19_multianno.vcf\" in line 7:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/snp_myanno\" in line 10:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 7:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 10:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/12_annovar_ind.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/norm_filter_indel_left_trim_combine_genotype.vcf\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/indel_myanno.hg19_multianno.vcf\" in line 7:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/indel_myanno\" in line 10:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 7:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 10:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmpebsle3xl/rules/13_snpEff.smk:\n * Absolute path \"/config.yaml\" in line 1:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/combine_genotype.g.vcf.gz\" in line 4:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/output/combine_genotype_snpEff.vcf\" in line 5:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 5:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule fa_index (line 5, /tmp/tmpebsle3xl/rules/00_fa_index.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule bam_index (line 5, /tmp/tmpebsle3xl/rules/00_bam_index.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule picard_dict (line 5, /tmp/tmpebsle3xl/rules/00_picard_dict.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule haplotype_caller (line 5, /tmp/tmpebsle3xl/rules/01_haplotype_caller.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule combine_gvcf (line 5, /tmp/tmpebsle3xl/rules/02_combine_gvcf.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule genotype_gvcf (line 5, /tmp/tmpebsle3xl/rules/03_genotype_gvcf.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable ref from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule left_trim (line 5, /tmp/tmpebsle3xl/rules/04_left_trim.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule select_snp (line 5, /tmp/tmpebsle3xl/rules/05_select_snp.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule select_indel (line 5, /tmp/tmpebsle3xl/rules/06_select_indel.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule snp_filter (line 5, /tmp/tmpebsle3xl/rules/07_filter_snp.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule indel_filter (line 5, /tmp/tmpebsle3xl/rules/08_filter_indel.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule bcftools_norm_snp (line 5, /tmp/tmpebsle3xl/rules/09_bcftools_norm_snp.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule bcftools_norm_ind (line 5, /tmp/tmpebsle3xl/rules/10_bcftools_norm_ind.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule anovar_snp (line 5, /tmp/tmpebsle3xl/rules/11_annovar_snp.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param vcf is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule anovar_ind (line 5, /tmp/tmpebsle3xl/rules/12_annovar_ind.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param vcf is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule snpEff_snp (line 5, /tmp/tmpebsle3xl/rules/13_snpEff.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 0, - "subscribers_count": 1, - "topics": [], - "updated_at": 1723453165.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": null, - "formatting": null, - "full_name": "bjoernellens1/pypsa-eur-project", - "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmplwxdek0h/Snakefile\", line 13, in \u003cmodule\u003e\n from scripts._helpers import path_provider, copy_default_files, get_scenarios, get_rdir\n\n File \"/tmp/tmplwxdek0h/scripts/_helpers.py\", line 23, in \u003cmodule\u003e\n from tqdm import tqdm\n\nModuleNotFoundError: No module named \u0027tqdm\u0027\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 0, - "subscribers_count": 1, - "topics": [], - "updated_at": 1723384817.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": "Snakemake workflow to map PacBio HiFi reads back to an assembly and check for misassemblies at specific regions via NucFlag.", - "formatting": null, - "full_name": "logsdon-lab/Snakemake-NucFlag", - "latest_release": "v0.1.0", - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmptyt7hvk6/logsdon-lab-Snakemake-NucFlag-9428dd5/workflow/Snakefile\", line 6, in \u003cmodule\u003e\n\n File \"/tmp/tmptyt7hvk6/logsdon-lab-Snakemake-NucFlag-9428dd5/workflow/rules/common.smk\", line 37, in get_sample_assemblies_and_reads\n for sm in config[\"samples\"]:\n ^^^^^^^^^^^^^^^^^^^\n\nKeyError: \u0027samples\u0027\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 0, - "subscribers_count": 0, - "topics": [], - "updated_at": 1723304315.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": "next step after recount-pump in the monorail pipeline", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpj8zjb2fc/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "langmead-lab/recount-unify", - "latest_release": null, - "linting": "need to pass values for \u0027gene_rejoin_mapping\u0027 and \u0027exon_rejoin_mapping\u0027 and \u0027sample_ids_file\u0027 and \u0027num_samples\u0027 for the initial rejoining part of the pipeline!\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 0, - "subscribers_count": 5, - "topics": [], - "updated_at": 1723235817.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp22brxynr/rules/demand.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp22brxynr/rules/model.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp22brxynr/rules/wind-and-solar.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp22brxynr/rules/doc.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp22brxynr/rules/biofuels.smk\": Formatted content is different from original\n[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\/\u0027\n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\/\u0027\n[DEBUG] In file \"/tmp/tmp22brxynr/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp22brxynr/rules/transmission.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp22brxynr/rules/nuclear.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp22brxynr/rules/hydro.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp22brxynr/rules/shapes.smk\": Formatted content is different from original\n[INFO] 10 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "calliope-project/euro-calliope-modular", - "latest_release": null, - "linting": "Using workflow specific profile profiles/default for setting default command line arguments.\n/tmp/tmp22brxynr/Snakefile:50: SyntaxWarning: invalid escape sequence \u0027\\/\u0027\n \n/tmp/tmp22brxynr/Snakefile:114: SyntaxWarning: invalid escape sequence \u0027\\/\u0027\n \"techs/supply/open-field-solar-and-wind-onshore.yaml\",\nLints for snakefile /tmp/tmp22brxynr/Snakefile:\n * Absolute path \"/\" if config[\" in line 8:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 30:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 54:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 72:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 89:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 100:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmp22brxynr/./rules/biofuels.smk:\n * Path composition with \u0027+\u0027 in line 57:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmp22brxynr/./rules/model.smk:\n * Path composition with \u0027+\u0027 in line 4:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmp22brxynr/./rules/transmission.smk:\n * Path composition with \u0027+\u0027 in line 26:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 44:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule units (line 1, /tmp/tmp22brxynr/./rules/shapes.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule units_without_shape (line 29, /tmp/tmp22brxynr/./rules/shapes.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule download_potentials (line 9, /tmp/tmp22brxynr/./rules/wind-and-solar.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule potentials (line 40, /tmp/tmp22brxynr/./rules/wind-and-solar.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule download_capacity_factors_wind_and_solar (line 92, /tmp/tmp22brxynr/./rules/wind-and-solar.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule area_to_capacity_limits (line 123, /tmp/tmp22brxynr/./rules/wind-and-solar.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule capacity_factors_onshore_wind_and_solar (line 161, /tmp/tmp22brxynr/./rules/wind-and-solar.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule download_eez (line 210, /tmp/tmp22brxynr/./rules/wind-and-solar.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule eez (line 241, /tmp/tmp22brxynr/./rules/wind-and-solar.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule shared_coast (line 287, /tmp/tmp22brxynr/./rules/wind-and-solar.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule capacity_factors_offshore (line 326, /tmp/tmp22brxynr/./rules/wind-and-solar.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule download_biofuel_potentials_and_costs (line 3, /tmp/tmp22brxynr/./rules/biofuels.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule preprocess_biofuel_potentials_and_cost (line 34, /tmp/tmp22brxynr/./rules/biofuels.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule biofuels (line 73, /tmp/tmp22brxynr/./rules/biofuels.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule biofuel_tech_module (line 123, /tmp/tmp22brxynr/./rules/biofuels.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_units (line 17, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_download_hydro_generation_data (line 69, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_download_pumped_hydro_data (line 102, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_download_runoff_data (line 135, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_download_basins_database (line 172, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_download_stations_database (line 205, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_basins_database (line 238, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_stations_database (line 269, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_preprocess_basins (line 309, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_preprocess_hydro_stations (line 345, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_inflow_m3 (line 382, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_inflow_mwh (line 417, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_hydro_capacities (line 457, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_hydro_capacity_factors_hydro (line 488, https://:ghs_DKQIOiILiBzBPq2C5hw99S2SJJKSF03TDHWk@raw.githubusercontent.com/calliope-project/ec_modules/feature-hydro/modules/hydro/workflow/rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule data_hydro (line 100, /tmp/tmp22brxynr/./rules/hydro.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule download_raw_load (line 4, /tmp/tmp22brxynr/./rules/demand.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule electricity_load_national (line 35, /tmp/tmp22brxynr/./rules/demand.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule electricity_load (line 71, /tmp/tmp22brxynr/./rules/demand.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule jrc_power_plant_database_zipped (line 1, /tmp/tmp22brxynr/./rules/nuclear.smk):\n * Do not access input and output files individually by index in shell commands:\n When individual access to input or output files is needed (i.e., just\n writing \u0027{input}\u0027 is impossible), use names (\u0027{input.somename}\u0027) instead\n of index based access.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#rules\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule jrc_power_plant_database (line 32, /tmp/tmp22brxynr/./rules/nuclear.smk):\n * Do not access input and output files individually by index in shell commands:\n When individual access to input or output files is needed (i.e., just\n writing \u0027{input}\u0027 is impossible), use names (\u0027{input.somename}\u0027) instead\n of index based access.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#rules\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule nuclear_regional_capacity (line 60, /tmp/tmp22brxynr/./rules/nuclear.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule model_input_locations (line 1, /tmp/tmp22brxynr/./rules/model.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule download_entsoe_tyndp_zip (line 4, /tmp/tmp22brxynr/./rules/transmission.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule entsoe_tyndp_xlsx (line 35, /tmp/tmp22brxynr/./rules/transmission.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule transmission_entsoe_tyndp_tech_module (line 70, /tmp/tmp22brxynr/./rules/transmission.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule transmission_linked_neighbours_tech_module (line 110, /tmp/tmp22brxynr/./rules/transmission.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_with_location_specific_data (line 91, /tmp/tmp22brxynr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_without_location_specific_data (line 134, /tmp/tmp22brxynr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule module_without_specific_data (line 147, /tmp/tmp22brxynr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule auxiliary_files (line 180, /tmp/tmp22brxynr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule model (line 213, /tmp/tmp22brxynr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule dag (line 290, /tmp/tmp22brxynr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule clean (line 311, /tmp/tmp22brxynr/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 0, - "subscribers_count": 3, - "topics": [], - "updated_at": 1723213764.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": "A Snakemake pipeline for copy number variant calling without normal tissue samples", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpzqunecdj/workflow/rules/mutect2.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpzqunecdj/workflow/rules/mask_ref.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpzqunecdj/workflow/rules/map_bowtie2.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpzqunecdj/workflow/rules/bcf.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpzqunecdj/workflow/rules/umi_mapping.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpzqunecdj/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpzqunecdj/workflow/rules/map_bwa.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpzqunecdj/workflow/rules/qc_map.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmpzqunecdj/workflow/rules/cnv_calling_with_true_pon.smk\": InvalidPython: Black error:\n```\nCannot parse: 54:0: \u003cline number missing in source\u003e\n```\n\n[DEBUG] In file \"/tmp/tmpzqunecdj/workflow/rules/cnv_calling_with_true_pon.smk\": \n[WARNING] In file \"/tmp/tmpzqunecdj/workflow/rules/cnvkit.smk\": Keyword \"shell\" at line 160 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmpzqunecdj/workflow/rules/cnvkit.smk\": Keyword \"params\" at line 316 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpzqunecdj/workflow/rules/cnvkit.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpzqunecdj/workflow/rules/purecn.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpzqunecdj/workflow/rules/stats.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpzqunecdj/workflow/rules/trimming_fastqc.smk\": Formatted content is different from original\n[INFO] 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] 12 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "pedricolino/cnakepit", - "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpzqunecdj/workflow/Snakefile\", line 30, in \u003cmodule\u003e\n samples = read_sample(config[\u0027data\u0027][\u0027samples_in_directory\u0027])\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1026, in read_csv\n return _read(filepath_or_buffer, kwds)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 620, in _read\n parser = TextFileReader(filepath_or_buffer, **kwds)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1620, in __init__\n self._engine = self._make_engine(f, self.engine)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1880, in _make_engine\n self.handles = get_handle(\n ^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/common.py\", line 873, in get_handle\n handle = open(\n ^^^^^\n\nFileNotFoundError: [Errno 2] No such file or directory: \u0027resources/data/sample_sheet.tsv\u0027\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 0, - "subscribers_count": 1, - "topics": [ - "bioinformatics", - "bwa", - "cna", - "cnv", - "cnvkit", - "conda", - "copynumbervariation", - "mutect2", - "panels", - "purecn", - "sequencing-data", - "snakemake", - "targeted-sequencing" - ], - "updated_at": 1723212951.0 - }, - { - "config_readme": "\u003cp\u003eDescribe how to configure the workflow (using config.yaml and maybe additional files).\nAll of them need to be present with example entries inside of the config folder.\u003c/p\u003e\n", - "data_format": 2, - "description": "Snakemake workflow to call denovo dna variants on a RIL population", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp9m5bzqwx/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "Bioinflows-Bioversity-CIAT/denovo-dna-variant-calling", - "latest_release": null, - "linting": null, - "mandatory_flags": { - "desc": null, - "flags": null - }, - "report": true, - "software_stack_deployment": { - "conda": true, - "singularity": false, - "singularity+conda": false - }, - "standardized": true, - "stargazers_count": 0, - "subscribers_count": 0, - "topics": [], - "updated_at": 1723209947.0 - }, - { - "config_readme": "\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eGeneral Configuration\u003c/h1\u003e\u003ca id=\"user-content-general-configuration\" class=\"anchor\" aria-label=\"Permalink: General Configuration\" href=\"#general-configuration\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eTo configure this workflow, modify \u003ccode\u003econfig/config.yaml\u003c/code\u003e according to your needs, following the explanations provided in the file.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eOutput folders\u003c/h2\u003e\u003ca id=\"user-content-output-folders\" class=\"anchor\" aria-label=\"Permalink: Output folders\" href=\"#output-folders\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eBy default, this workflow stores the files obtained, parsed and aggregated into three different folders (\u003ccode\u003edownloaded/\u003c/code\u003e, \u003ccode\u003eparsed/\u003c/code\u003e \u003ccode\u003eaggregated/\u003c/code\u003e) in the working directory. This behavior can be changed with the entries \u003ccode\u003edownloaded_mriot_dir:\u003c/code\u003e, \u003ccode\u003eparsed_mriot_dir:\u003c/code\u003e and \u003ccode\u003eaggregated_mriot_dir:\u003c/code\u003e.\u003c/p\u003e\n\u003cp\u003eFiles corresponding to a specific MRIOT will be stored in a subfolder of the corresponding name. For instance, Exiobase 3 (in ixi system) for year 1995 aggregated to 74 sectors will be stored under \u003ccode\u003eparsed/exiobase3_ixi/exiobase3_ixi_1995_74_sectors.pkl\u003c/code\u003e.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eSector aggregation files\u003c/h2\u003e\u003ca id=\"user-content-sector-aggregation-files\" class=\"anchor\" aria-label=\"Permalink: Sector aggregation files\" href=\"#sector-aggregation-files\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThe workflow looks for aggregation files in the \u003ccode\u003eaggregation_csv_dir:\u003c/code\u003e (\u003ccode\u003econfig/aggregation_files\u003c/code\u003e) by default.\u003c/p\u003e\n\u003cp\u003eSome existing aggregation are included in the repository, and new ones can be added. If you think an aggregation file you designed would be a valuable contribution, don\u0027t hesitate to pull-request it !\u003c/p\u003e\n\u003cp\u003eThe folder structure follows the same as for outputs, for instance, the file used to aggregate Exiobase 3 to 74 sectors is looked under \u003ccode\u003econfig/aggregation_files/exiobase3_ixi/exiobase3_ixi_74_sectors.csv\u003c/code\u003e\u003c/p\u003e\n\u003cp\u003eFiles should be in csv format, with a first column \u003ccode\u003esector\u003c/code\u003e with all the original sectors of the MRIOT, and \u003ccode\u003egroup\u003c/code\u003e and \u003ccode\u003ename\u003c/code\u003e columns with the new ID and names to map the original sectors too.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eCommon aggregation\u003c/h2\u003e\u003ca id=\"user-content-common-aggregation\" class=\"anchor\" aria-label=\"Permalink: Common aggregation\" href=\"#common-aggregation\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eAs an additional way to aggregate different MRIOTs into a common one, this workflow also embarks a \u003ccode\u003econfig/aggregation_files/sectors_common_aggreg.ods\u003c/code\u003e file for this purpose.\u003c/p\u003e\n\u003cp\u003eThe sheet \u003ccode\u003ecommon_aggreg\u003c/code\u003e of the file defines the sector to aggregate to via \u003ccode\u003egroup_id\u003c/code\u003e and \u003ccode\u003esector_name\u003c/code\u003e columns. The following sheets, \u003ccode\u003e\u0026lt;mriot_name\u0026gt;_to_common_aggreg\u003c/code\u003e, have \u003ccode\u003eoriginal sector\u003c/code\u003e, \u003ccode\u003eto_id\u003c/code\u003e and a \u003ccode\u003enew sector\u003c/code\u003e columns auto computed from \u003ccode\u003eto_id\u003c/code\u003e.\u003c/p\u003e\n\u003cp\u003eAsking the workflow to build \u003ccode\u003eaggregated/icio2021/icio2021_2003_common_aggreg.pkl\u003c/code\u003e, for instance, will aggregate \u003ccode\u003eicio2021_2003_full.pkl\u003c/code\u003e to the sectors defined in the sheet \u003ccode\u003ecommon_aggreg\u003c/code\u003e based on the correspondence in \u003ccode\u003eicio2021_to_common_aggreg\u003c/code\u003e.\u003c/p\u003e\n\u003cp\u003eDisclaimer: This work is still under progress and still requires to be streamlined.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eParameters aggregation\u003c/h2\u003e\u003ca id=\"user-content-parameters-aggregation\" class=\"anchor\" aria-label=\"Permalink: Parameters aggregation\" href=\"#parameters-aggregation\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThe workflow also allows to build sector parameters files for the \u003ccode\u003eBoARIO\u003c/code\u003e model.\nWe provide a \u003ccode\u003econfig/mriot_params/exiobase3_ixi_full_sectors.csv\u003c/code\u003e \"master\" file that contains values we used with the model and this MRIOT, and from which similar files can be obtained for the other MRIOT, using \u003ccode\u003econfig/aggregation_files/exiobase3_ixi/exiobase3_ixi_to_other_mrio_sectors.ods\u003c/code\u003e.\u003c/p\u003e\n", - "data_format": 2, - "description": "Pipelines to parse and aggregate MRIOT data for BoARIO", - "formatting": "[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpfciba8yw/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpfciba8yw/workflow/rules/mrio_treatments.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpfciba8yw/workflow/rules/sectors_config.smk\": Formatted content is different from original\n[INFO] 3 file(s) would be changed \ud83d\ude2c\n[INFO] 4 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", - "full_name": "spjuhel/BoARIO-MRIOT-Tools", - "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpfciba8yw/workflow/Snakefile\", line 6, in \u003cmodule\u003e\n from boario_tools.regex_patterns import (\n\nModuleNotFoundError: No module named \u0027boario_tools\u0027\n\n", - "mandatory_flags": { - "desc": null, - "flags": null - }, - "report": false, - "software_stack_deployment": { - "conda": true, - "singularity": false, - "singularity+conda": false - }, - "standardized": true, - "stargazers_count": 0, - "subscribers_count": 1, - "topics": [], - "updated_at": 1723205425.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": "Snakemake workflow for scoring and comparing multiple bacterial genome assemblies (Illumina, Nanopore) to reference genome(s). ", - "formatting": null, - "full_name": "pmenzel/score-assemblies-MIT", - "latest_release": "v1.2", - "linting": null, - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 0, - "subscribers_count": 1, - "topics": [ - "bacterial-genome-analysis", - "bioinformatics-pipeline", - "nanopore-sequencing", - "snakemake" - ], - "updated_at": 1723619591.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": "Snakemake workflow for bacterial genome assembly + polishing for Oxford Nanopore (ONT) sequencing using multiple tools.", - "formatting": null, - "full_name": "pmenzel/ont-assembly-snake-MIT", - "latest_release": "v1.4", - "linting": "Lints for snakefile /tmp/tmp5o1hg4iz/pmenzel-ont-assembly-snake-MIT-69fcb11/Snakefile:\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n * Path composition with \u0027+\u0027 in line 54:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 58:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 6:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 28:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 54:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 56:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 58:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 63:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 67:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule filtlong (line 227, /tmp/tmp5o1hg4iz/pmenzel-ont-assembly-snake-MIT-69fcb11/Snakefile):\n * Shell command directly uses variable filtlong_min_read_length from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule filtlongMB (line 272, /tmp/tmp5o1hg4iz/pmenzel-ont-assembly-snake-MIT-69fcb11/Snakefile):\n * Shell command directly uses variable filtlong_min_read_length from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule filtlongPC (line 318, /tmp/tmp5o1hg4iz/pmenzel-ont-assembly-snake-MIT-69fcb11/Snakefile):\n * Shell command directly uses variable filtlong_min_read_length from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule filtlongMBql (line 363, /tmp/tmp5o1hg4iz/pmenzel-ont-assembly-snake-MIT-69fcb11/Snakefile):\n * Shell command directly uses variable filtlong_min_read_length from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule canu (line 918, /tmp/tmp5o1hg4iz/pmenzel-ont-assembly-snake-MIT-69fcb11/Snakefile):\n * Shell command directly uses variable target_genome_size from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 0, - "subscribers_count": 1, - "topics": [ - "bacterial-genome-analysis", - "bioinformatics", - "bioinformatics-pipeline", - "nanopore-sequencing", - "snakemake", - "snakemake-workflow" - ], - "updated_at": 1723619513.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": "A snakemake-based workflow for converting Illumina\u0027s bcl files to fastq files with the option of further downstream analysis (using FastQC, STAR+RSeQC, cutadapt) and encryption via gocryptfs", - "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmp690v5jwz/rules/pe_processing.smk\": Keyword \"input\" at line 135 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[ERROR] In file \"/tmp/tmp690v5jwz/rules/pe_processing.smk\": InvalidPython: Black error:\n```\nCannot parse: 143:4: log:\n```\n\n[DEBUG] In file \"/tmp/tmp690v5jwz/rules/pe_processing.smk\": \n[DEBUG] In file \"/tmp/tmp690v5jwz/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmp690v5jwz/rules/fastqProcessing.smk\": Keyword \"input\" at line 196 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmp690v5jwz/rules/fastqProcessing.smk\": Keyword \"input\" at line 226 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmp690v5jwz/rules/fastqProcessing.smk\": Keyword \"output\" at line 379 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmp690v5jwz/rules/fastqProcessing.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp690v5jwz/rules/bcl2fastq.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp690v5jwz/rules/qcShort.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmp690v5jwz/Snakefile\": InvalidPython: Black error:\n```\nCannot parse: 1:6: needs to be here for the snakemake workflow catalogue\n\n(Note reported line number may be incorrect, as snakefmt could not determine the true line number)\n```\n\n[DEBUG] In file \"/tmp/tmp690v5jwz/Snakefile\": \n[WARNING] In file \"/tmp/tmp690v5jwz/rules/convert2fastq.smk\": Keyword \"output\" at line 95 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmp690v5jwz/rules/convert2fastq.smk\": Keyword \"output\" at line 114 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[ERROR] In file \"/tmp/tmp690v5jwz/rules/convert2fastq.smk\": NoParametersError: L170: In input definition.\n[DEBUG] In file \"/tmp/tmp690v5jwz/rules/convert2fastq.smk\": \n[DEBUG] In file \"/tmp/tmp690v5jwz/rules/qc.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp690v5jwz/rules/qc_pe.smk\": Formatted content is different from original\n[INFO] 3 file(s) raised parsing errors \ud83e\udd15\n[INFO] 6 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "WestGermanGenomeCenter/bcl2fastq2_Pipeline", - "latest_release": null, - "linting": "SyntaxError in file /tmp/tmp690v5jwz/Snakefile, line 1:\ninvalid syntax:\nneeds to be here for the snakemake workflow catalogue\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 0, - "subscribers_count": 1, - "topics": [], - "updated_at": 1723118553.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": "Mapping of RNAseq reads to sequences obtained from CryoEM in Toxoplasma gondii", - "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmpdpo1e4ok/Snakefile\": Keyword \"input\" at line 362 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpdpo1e4ok/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "glaParaBio/cryoem-mitoribosome-rnaseq", - "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpdpo1e4ok/Snakefile\", line 7, in \u003cmodule\u003e\n TGMITO = os.path.basename(config[\u0027tgmito\u0027])\n ^^^^^^^^^^^^\n\nKeyError: \u0027tgmito\u0027\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 0, - "subscribers_count": 1, - "topics": [], - "updated_at": 1723114523.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": "Multiplex Accurate Sensitive Quantitation (MASQ) analysis and primer design", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp_kkyaebk/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "amoffitt/MASQ", - "latest_release": null, - "linting": "Lints for snakefile /tmp/tmp_kkyaebk/Snakefile:\n * Absolute path \"/r1.fastq.gz\" in line 143:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/r2.fastq.gz\" in line 144:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/r1.fastq.gz\" in line 176:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/r2.fastq.gz\" in line 177:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/extended_var_table.txt\" in line 178:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Absolute path \"/extended_var_table.txt\" in line 223:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Path composition with \u0027+\u0027 in line 65:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 178:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 223:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 72:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 110:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 425:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 426:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule convert_SNV_table (line 122, /tmp/tmp_kkyaebk/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule barcode_split (line 150, /tmp/tmp_kkyaebk/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Param output_dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule fastqc (line 184, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule check_loci_extend_and_plot (line 219, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule sort_data_by_tag_and_locus (line 255, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule all_base_report (line 310, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule combine_within_tag_errors (line 361, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule tag_count_graphs_per_region (line 390, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule tag_count_graphs_combined (line 426, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule rollup_tags (line 461, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule combine_reports_alignment (line 501, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule combine_reports_basecount (line 530, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule combine_reports_per_base (line 558, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule combine_reports_rollup (line 586, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule combine_reports_readspertag (line 614, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule extract_variant_bases_from_report (line 643, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule plot_rollup_results (line 671, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule final_report (line 704, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule bad_loci (line 735, /tmp/tmp_kkyaebk/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule qc_plots (line 749, /tmp/tmp_kkyaebk/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n\nLints for rule filter_base_report (line 776, /tmp/tmp_kkyaebk/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 0, - "subscribers_count": 1, - "topics": [], - "updated_at": 1723065291.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": "Significantly improved bam2bakR implementation", - "formatting": null, - "full_name": "isaacvock/fastq2EZbakR", - "latest_release": null, - "linting": null, - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 0, - "subscribers_count": 1, - "topics": [], - "updated_at": 1723042307.0 - }, - { - "config_readme": "\u003cp\u003eThis pipeline requires two configuration file:\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003e\u003ccode\u003econfig.yaml\u003c/code\u003e\u003c/h1\u003e\u003ca id=\"user-content-configyaml\" class=\"anchor\" aria-label=\"Permalink: config.yaml\" href=\"#configyaml\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eA standard \u003ccode\u003eSnakemake\u003c/code\u003e configuration, yaml-formatted file containing a list of\nall parameters accepted in this workflow:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003esamples\u003c/code\u003e: Path to the file containing link between samples and their fastq file(s)\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003eparams\u003c/code\u003e: Per-tool list of optional parameters\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eExample:\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003esamples: config/samples.csv\n\n# Optional parameters\nparams:\n fair_bowtie2_mapping:\n bowtie2:\n # Optional parameters for bowtie2-build\n build: \"\"\n # Optional parameters for bowtie2-align\n align: \"\"\n sambamba:\n # Optional parameters for sambamba view\n view: \"--format \u0027bam\u0027 --filter \u0027mapping_quality \u0026gt;= 30 and not (unmapped or mate_is_unmapped)\u0027 \"\n # Optional parameters for sambamba markdup\n markdup: \"--remove-duplicates\"\n picard:\n # Mapping QC optional parameters\n metrics: \"\"\n\u003c/code\u003e\u003c/pre\u003e\n\u003cp\u003eA complete list of accepted keys is available \u003ca href=\"https://github.com/tdayris/fair_bowtie2_mapping/blob/main/workflow/schemas/config.schema.yaml\"\u003ein schemas\u003c/a\u003e,\nwith their default value, expected type, and human readable description.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003e\u003ccode\u003esamples.csv\u003c/code\u003e\u003c/h1\u003e\u003ca id=\"user-content-samplescsv\" class=\"anchor\" aria-label=\"Permalink: samples.csv\" href=\"#samplescsv\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eA CSV-formatted text file containing the following mandatory columns:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003esample_id\u003c/code\u003e: Unique name of the sample\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003eupstream_file\u003c/code\u003e: Path to upstream fastq file\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003especies\u003c/code\u003e: The species name, according to Ensembl standards\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003ebuild\u003c/code\u003e: The corresponding genome build, according to Ensembl standards\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003erelease\u003c/code\u003e: The corresponding genome release, according to Ensembl standards\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003edownstream_file\u003c/code\u003e: Optional path to downstream fastq file\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eExample:\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003esample_id,upstream_file,downstream_file,species,build,release\nsac_a,data/reads/a.scerevisiae.1.fq,data/reads/a.scerevisiae.2.fq,saccharomyces_cerevisiae,R64-1-1,110\n\u003c/code\u003e\u003c/pre\u003e\n\u003cp\u003eA complete list of accepted keys is available \u003ca href=\"https://github.com/tdayris/fair_bowtie2_mapping/blob/main/workflow/schemas/samples.schema.yaml\"\u003ein schemas\u003c/a\u003e,\nwith their default value, expected type, and human readable description.\u003c/p\u003e\n\u003cp\u003eWhile \u003ccode\u003eCSV\u003c/code\u003e format is tested and recommended, this workflow uses python\n\u003ccode\u003ecsv.Sniffer()\u003c/code\u003e to detect column separator. Tabulation and semicolumn are\nalso accepted as field separator. Remember that only comma-separator is\ntested.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003e\u003ccode\u003egenomes.csv\u003c/code\u003e\u003c/h1\u003e\u003ca id=\"user-content-genomescsv\" class=\"anchor\" aria-label=\"Permalink: genomes.csv\" href=\"#genomescsv\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThis file is fully optional. When missing, the genome sequences\nwill be downloaded from Ensembl and indexed.\u003c/p\u003e\n\u003cp\u003eA CSV-formatted text file containing the following mandatory columns:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003especies\u003c/code\u003e: The species name, according to Ensembl standards\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003ebuild\u003c/code\u003e: The corresponding genome build, according to Ensembl standards\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003erelease\u003c/code\u003e: The corresponding genome release, according to Ensembl standards\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eThe following columns are optional and are used to avoid downloading genomes:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003efasta\u003c/code\u003e: Path to the reference genome sequence (FASTA formatted)\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003efasta_index\u003c/code\u003e: Path to the reference genome sequence index (FAI formatted)\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003ebowtie2_dna_index\u003c/code\u003e: Path to the main directory containing reference index\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eExample:\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003especies,build,release,fasta,fasta_index,bowtie2_index\nhomo_sapiens,GRCh38,110,/path/to/sequence.fasta,/path/to/sequence.fasta.fai,/path/to/bowtie2_sequence/\nmus_musculus,GRCm38,99,,,\nmus_musculus,GRCm39,110,,,\n\u003c/code\u003e\u003c/pre\u003e\n\u003cp\u003eA complete list of accepted keys is available \u003ca href=\"https://github.com/tdayris/fair_bowtie2_mapping/blob/main/workflow/schemas/genomes.schema.yaml\"\u003ein schemas\u003c/a\u003e,\nwith their default value, expected type, and human readable description.\u003c/p\u003e\n\u003cp\u003eWhile \u003ccode\u003eCSV\u003c/code\u003e format is tested and recommended, this workflow uses python\n\u003ccode\u003ecsv.Sniffer()\u003c/code\u003e to detect column separator. Tabulation and semicolumn are\nalso accepted as field separator. Remember that only comma-separator is\ntested.\u003c/p\u003e\n", - "data_format": 2, - "description": "Align reads over a reference genome, filter aligned-reads, and mark duplicates", - "formatting": null, - "full_name": "tdayris/fair_bowtie2_mapping", - "latest_release": "4.2.0", - "linting": null, - "mandatory_flags": { - "desc": "Align ungapped reads to the genome with Bowtie2", - "flags": null - }, - "report": true, - "software_stack_deployment": { - "conda": true, - "singularity": false, - "singularity+conda": true - }, - "standardized": true, - "stargazers_count": 0, - "subscribers_count": 1, - "topics": [ - "bowtie2", - "multiqc", - "sambamba", - "snakemake", - "snakemake-workflow", - "snakemake-wrappers" - ], - "updated_at": 1723031584.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\d\u0027\n[DEBUG] In file \"/tmp/tmp8pqah41f/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "jorgenriseth/gMRI2FEM", - "latest_release": null, - "linting": "/tmp/tmp8pqah41f/Snakefile:32: SyntaxWarning: invalid escape sequence \u0027\\d\u0027\n SUBJECTS=config[\"subjects\"]\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp8pqah41f/Snakefile\", line 14, in \u003cmodule\u003e\n + \"conda activate $CONDA_ENV_NAME \u0026\u0026 \"\n ^^^^^^^^^^^^^^^^^^^^^^^^^^\n\nAttributeError: \u0027Workflow\u0027 object has no attribute \u0027use_singularity\u0027\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 0, - "subscribers_count": 1, - "topics": [], - "updated_at": 1723028673.0 - }, { "config_readme": null, "data_format": 2, @@ -4793,23 +4810,6 @@ var data = "topics": [], "updated_at": 1722953693.0 }, - { - "config_readme": null, - "data_format": 2, - "description": "Snakemake workflow to analyse hematological malignancies in whole genome data", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/rules/cnvkit.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/rules/mutectcaller_to_tsv.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/rules/fix_af.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/rules/peddy_create_ped.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/rules/export.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/rules/dux4_rearrangements.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/rules/manta_to_tsv.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/rules/sample_order_multiqc.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/rules/gatk_cnv_denoise_read_counts_by_sex.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/rules/cnvkit_table.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/rules/html_output.smk\": Formatted content is different from original\n[INFO] 13 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "clinical-genomics-uppsala/fluffy_hematology_wgs", - "latest_release": "v1.1.0", - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/Snakefile\", line 7, in \u003cmodule\u003e\n include: \"rules/common.smk\"\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp9r39_3kn/clinical-genomics-uppsala-fluffy_hematology_wgs-f1a96f0/workflow/rules/common.smk\", line 12, in \u003cmodule\u003e\n from hydra_genetics.utils.resources import load_resources\n\nModuleNotFoundError: No module named \u0027hydra_genetics\u0027\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 0, - "subscribers_count": 2, - "topics": [], - "updated_at": 1723713011.0 - }, { "config_readme": null, "data_format": 2, @@ -36777,6 +36777,278 @@ var data = "topics": [], "updated_at": 1614368088.0 }, + { + "config_readme": null, + "data_format": 2, + "description": "Workflow for merging multi-lane fastq files from the Illumina NextSeq 550 using Snakemake. In addition, basic QC and md5 checksums are generated.", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmplqdsifer/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "GenoMixer/illumina-snakemake-nextseq-pipeline", + "latest_release": null, + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmplqdsifer/Snakefile\", line 19, in \u003cmodule\u003e\n samples=pd.read_csv(\"SampleSheet.csv\",skiprows=16).set_index(\"Sample_ID\")\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1026, in read_csv\n return _read(filepath_or_buffer, kwds)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 620, in _read\n parser = TextFileReader(filepath_or_buffer, **kwds)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1620, in __init__\n self._engine = self._make_engine(f, self.engine)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1880, in _make_engine\n self.handles = get_handle(\n ^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/common.py\", line 873, in get_handle\n handle = open(\n ^^^^^\n\nFileNotFoundError: [Errno 2] No such file or directory: \u0027SampleSheet.csv\u0027\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 1, + "subscribers_count": 1, + "topics": [], + "updated_at": 1723712151.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": "INSinPAL : Detecting Large Insertion Events in Whole Genome Sequencing Data at Palindromic Fragile Sites for Diagnostic Purposes", + "formatting": "[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\|\u0027\n[DEBUG] In file \"/tmp/tmpyjkqi307/Meetmet21-INSinPAL-d4d6e37/workflow/rules/mine_palindromes_in_genome.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyjkqi307/Meetmet21-INSinPAL-d4d6e37/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyjkqi307/Meetmet21-INSinPAL-d4d6e37/workflow/rules/add_mate_score_tags.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyjkqi307/Meetmet21-INSinPAL-d4d6e37/workflow/rules/estimate_size_annotsv.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyjkqi307/Meetmet21-INSinPAL-d4d6e37/workflow/rules/call_INS_SVs.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyjkqi307/Meetmet21-INSinPAL-d4d6e37/workflow/rules/select_interesting_INS.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyjkqi307/Meetmet21-INSinPAL-d4d6e37/workflow/rules/annotate_MEIs_sourceINS.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyjkqi307/Meetmet21-INSinPAL-d4d6e37/workflow/rules/merge_callers.smk\": Formatted content is different from original\n[INFO] 8 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "Meetmet21/INSinPAL", + "latest_release": "v1.0.0", + "linting": "/tmp/tmpyjkqi307/Meetmet21-INSinPAL-d4d6e37/workflow/rules/mine_palindromes_in_genome.smk:137: SyntaxWarning: invalid escape sequence \u0027\\|\u0027\n/tmp/tmpyjkqi307/Meetmet21-INSinPAL-d4d6e37/workflow/rules/mine_palindromes_in_genome.smk:156: SyntaxWarning: invalid escape sequence \u0027\\|\u0027\nCreateRuleException in file /tmp/tmpyjkqi307/Meetmet21-INSinPAL-d4d6e37/workflow/Snakefile, line 157:\nThe name all is already used by another rule\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 1, + "subscribers_count": 1, + "topics": [], + "updated_at": 1723711860.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": "Snakemake workflow to perform Energy Landscape Analysis", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmppbo4u2oi/chiba-ai-med-Landscaper-56700b3/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "chiba-ai-med/Landscaper", + "latest_release": "v1.6.1", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmppbo4u2oi/chiba-ai-med-Landscaper-56700b3/Snakefile\", line 11, in \u003cmodule\u003e\n INPUT = config[\"input\"]\n ~~~~~~^^^^^^^^^^\n\nKeyError: \u0027input\u0027\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 1, + "subscribers_count": 1, + "topics": [], + "updated_at": 1723617533.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": null, + "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmpzad5rp58/Snakefile\": Keyword \"input\" at line 140 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpzad5rp58/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "agma0/pypsa-za", + "latest_release": null, + "linting": "localrules directive specifies rules that are not present in the Snakefile:\n\tplot_network\n\nLints for snakefile /tmp/tmpzad5rp58/Snakefile:\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 91:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 95:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule build_inflow_per_country (line 111, /tmp/tmpzad5rp58/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule build_topology (line 142, /tmp/tmpzad5rp58/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule base_network (line 169, /tmp/tmpzad5rp58/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule add_electricity (line 264, /tmp/tmpzad5rp58/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule prepare_network (line 298, /tmp/tmpzad5rp58/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule solve_network (line 328, /tmp/tmpzad5rp58/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule plot_network_sa (line 364, /tmp/tmpzad5rp58/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 1, + "subscribers_count": 1, + "topics": [], + "updated_at": 1723498634.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": "Snakemake workflow to profile MHC-I neoepitopes with bulk tumor RNAseq data", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpwtunpk31/workflow/rules/index.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpwtunpk31/workflow/rules/alignment.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpwtunpk31/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpwtunpk31/workflow/rules/HLA_typing.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpwtunpk31/workflow/rules/base_recalibration.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpwtunpk31/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpwtunpk31/workflow/rules/pMHC.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpwtunpk31/workflow/rules/bam_cleaning.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpwtunpk31/workflow/rules/annotate_variants.smk\": Keyword \"input\" at line 15 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmpwtunpk31/workflow/rules/annotate_variants.smk\": Keyword \"shell\" at line 38 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpwtunpk31/workflow/rules/annotate_variants.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpwtunpk31/workflow/rules/quantification.smk\": Formatted content is different from original\n[INFO] 10 file(s) would be changed \ud83d\ude2c\n[INFO] 3 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", + "full_name": "danilotat/RNA-neoflow", + "latest_release": null, + "linting": null, + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 1, + "subscribers_count": 2, + "topics": [ + "bioinformatics", + "cancer-genomics", + "transcriptomics", + "immunology", + "neoepitopes" + ], + "updated_at": 1723471162.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": "Collection of scripts for benchmarking of seq2squiggle with other nanopore sequencing simulators", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpgku15z1q/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpgku15z1q/workflow/Snakefile\": Formatted content is different from original\n[INFO] 2 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "ZKI-PH-ImageAnalysis/seq2squiggle-benchmark", + "latest_release": null, + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpgku15z1q/workflow/Snakefile\", line 31, in \u003cmodule\u003e\n include: \"rules/d-melanogaster-genome-mode/benchmark.smk\"\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpgku15z1q/workflow/rules/d-melanogaster-genome-mode/input.smk\", line 5, in \u003cmodule\u003e\n HTTP = HTTPRemoteProvider()\n ^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/remote/__init__.py\", line 8, in __init__\n raise NotImplementedError(\n\nNotImplementedError: Remote providers have been replaced by Snakemake storage plugins. Please use the corresponding storage plugin instead (snakemake-storage-plugin-*).\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 1, + "subscribers_count": 0, + "topics": [], + "updated_at": 1724596451.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": "iSofOrmS annoTAtoR pipeline", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpe23jncir/workflow/rules/stringtie.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpe23jncir/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpe23jncir/workflow/rules/gtf_processing.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpe23jncir/workflow/rules/minimap2.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpe23jncir/workflow/rules/annotation.smk\": Formatted content is different from original\n[INFO] 5 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "LBGC-CFB/SOSTAR", + "latest_release": null, + "linting": "WorkflowError:\nWorkflow defines configfile ../config/config.yaml but it is not present or accessible (full checked path: /tmp/config/config.yaml).\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 1, + "subscribers_count": 1, + "topics": [ + "longread", + "rnaseq-pipeline" + ], + "updated_at": 1723450472.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": "HMMER-based microcin search using full microcin sequences and double-glycine signal region.", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpbbglp1gz/AaronFeller-Cinful_v2-5142ba7/workflow/rules/01_ORF_finding.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpbbglp1gz/AaronFeller-Cinful_v2-5142ba7/workflow/rules/03_merge_hmmsearch.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpbbglp1gz/AaronFeller-Cinful_v2-5142ba7/workflow/rules/06_clean_outputs.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpbbglp1gz/AaronFeller-Cinful_v2-5142ba7/workflow/rules/05_signal_hmm.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpbbglp1gz/AaronFeller-Cinful_v2-5142ba7/workflow/rules/04_analyze_outputs.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpbbglp1gz/AaronFeller-Cinful_v2-5142ba7/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpbbglp1gz/AaronFeller-Cinful_v2-5142ba7/workflow/rules/02_microcin_hmm.smk\": Formatted content is different from original\n[INFO] 7 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "AaronFeller/Cinful_v2", + "latest_release": "2.1", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpbbglp1gz/AaronFeller-Cinful_v2-5142ba7/workflow/Snakefile\", line 8, in \u003cmodule\u003e\n include: \"rules/01_ORF_finding.smk\"\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpbbglp1gz/AaronFeller-Cinful_v2-5142ba7/workflow/rules/01_ORF_finding.smk\", line 10, in \u003cmodule\u003e\n # Edit the contig names in the protein fasta files\n ^^^^^^^^^^^^^^^^^^^\n\nKeyError: \u0027outdir\u0027\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 1, + "subscribers_count": 1, + "topics": [ + "antimicrobial-peptides", + "bacterial-genome-analysis", + "bioinformatics-pipeline", + "blast", + "hidden-markov-model", + "hmm", + "hmmer", + "hmmer3", + "search", + "microcin" + ], + "updated_at": 1724756094.0 + }, + { + "config_readme": "\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eWorkflow configuration\u003c/h1\u003e\u003ca id=\"user-content-workflow-configuration\" class=\"anchor\" aria-label=\"Permalink: Workflow configuration\" href=\"#workflow-configuration\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eConfiguration is done via the \u003ccode\u003econfig\u003c/code\u003e folder content.\u003c/p\u003e\n\u003cp\u003eIt requires a \u003ccode\u003econfig.yaml\u003c/code\u003e file, and at least one \u003ccode\u003eflood_scenarios/\u0026lt;flood-scenario\u0026gt;.yaml\u003c/code\u003e file and one \u003ccode\u003esimulations/\u0026lt;simulation-scenario\u0026gt;.yaml\u003c/code\u003e, which are described in following sections. The GitHub repository contains examples of such files that should be used as templates.\u003c/p\u003e\n\u003cp\u003eIt also requires a \u003ccode\u003emriot_params\u003c/code\u003e directory for the MRIOT handling sub-module for which you can find documentation \u003ca href=\"https://github.com/spjuhel/BoARIO-MRIOT-Tools\"\u003ehere\u003c/a\u003e.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003e\u003ccode\u003econfig.yaml\u003c/code\u003e\u003c/h2\u003e\u003ca id=\"user-content-configyaml\" class=\"anchor\" aria-label=\"Permalink: config.yaml\" href=\"#configyaml\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThis file governs the high-level configuration of the pipeline (i.e. paths, notably to other configurations files, experiences to run, variables to store, etc.)\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003eTesting\u003c/h3\u003e\u003ca id=\"user-content-testing\" class=\"anchor\" aria-label=\"Permalink: Testing\" href=\"#testing\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eTo enforce testing before using the pipeline the file contains a \u003ccode\u003etesting: True\u003c/code\u003e statement, which we suggest you keep and override when running the pipeline by using the \u003ccode\u003e--config testing=False\u003c/code\u003e flag when invoking snakemake.\u003c/p\u003e\n\u003cp\u003ecreate_flood_scenarios_csv.py\ncreate_simspace_csv.py\ngenerate_local_results_rst.py\ngenerate_mrio_compare.py\ngenerate_results_index_rst.py\ngenerate_results_rst.py\nplot_results.py\nprep_plot_df.py\nregroup_aggreg.py\nsimulate.py\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003eMRIOT-Tools sub-module configuration\u003c/h3\u003e\u003ca id=\"user-content-mriot-tools-sub-module-configuration\" class=\"anchor\" aria-label=\"Permalink: MRIOT-Tools sub-module configuration\" href=\"#mriot-tools-sub-module-configuration\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThis part of the configuration give the required details for the MRIOTs-Tools sub-module and essentially governs\nwhere MRIOTs data should be looked for and stored. We suggest to keep it as is in most cases.\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003eprefix\u003c/code\u003e is the sub-directory of the pipeline global output which contains everything related to the sub-module. This is where the sub-module looks for configuration files and where it store the MRIOTs data.\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003eXXX_dir\u003c/code\u003e are the sub-sub-folders where corresponding data is to be found/stored\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003ecommon_aggreg\u003c/code\u003e is the name of the aggregation common to all MRIOTs\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003emriot_base_aggreg\u003c/code\u003e is the name of the initial, not aggregated MRIOT for each table type.\u003c/li\u003e\n\u003c/ul\u003e\n\u003cpre\u003e\u003ccode\u003edata-mriot:\n prefix: \"mriot_data/\"\n downloaded_mriot_dir: \"downloaded\"\n parsed_mriot_dir: \"parsed\"\n aggregated_mriot_dir: \"parsed\"\n mriot_params_dir: \"config/mriot_params\"\n\n common_aggreg: \"common_sectors_common_regions\"\n mriot_base_aggreg:\n exiobase3_ixi : \"full_sectors_full_regions\"\n exiobase3_pxp : \"full_sectors_full_regions\"\n eora26: \"full_no_reexport_sectors_full_regions\"\n euregio: \"full_sectors_full_regions\"\n\n\u003c/code\u003e\u003c/pre\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003eScenarios files\u003c/h3\u003e\u003ca id=\"user-content-scenarios-files\" class=\"anchor\" aria-label=\"Permalink: Scenarios files\" href=\"#scenarios-files\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eNext the file should define the scenarios to run, for instance:\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003eflood scenario: flood_scenarios/germany21.yaml\nsimulation space test: simulations/test.yaml\nsimulation space: simulations/germany21.yaml\n\u003c/code\u003e\u003c/pre\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch4 class=\"heading-element\"\u003eFlood scenarios\u003c/h4\u003e\u003ca id=\"user-content-flood-scenarios\" class=\"anchor\" aria-label=\"Permalink: Flood scenarios\" href=\"#flood-scenarios\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eFlood scenarios define the direct impact for each MRIOTs. Format is the following:\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003ename: \u0026lt;name of the scenario\u0026gt;\n\nyear: \u0026lt;year of the impact\u0026gt;\nunit: \u0026lt;monetary unit\u0026gt; (\"euro\", \"dollar\", ...)\nprod_cap_impact_unit: \u0026lt;unit value of impact on productive capital\u0026gt;\nhouse_impact_unit: \u0026lt;unit value of impact on households capital\u0026gt; (Can be 0)\nestimated_gdp_unit: \u0026lt;unit value of GDP of the whole region impacted\u0026gt; Used to translate the impact in relative terms\n\nduration: \u0026lt;duration of the event\u0026gt;\n\n# name of the country affected in each of the MRIOTs\ncountries_affected:\n exiobase3_ixi: \"DE\"\n eora26: \"DEU\"\n euregio: \"DE\"\n\n# name of the regions affected in each of the MRIOTs : share of the impact\n# this is mainly for euregio where there subregions are impacted\n# should also have a \"common\" element if you wish to run simulation on\n# the aggregated version of the MRIOTs\nregions_affected:\n exiobase3_ixi:\n \"DE\": 1.\n eora26:\n \"DEU\" : 1.\n euregio:\n \u0027DE21\u0027 : 0.00137977016177574\n \u0027DE22\u0027 : 0.00137977016177574\n \u0027DE23\u0027 : 0.00137977016177574\n [...]\n common:\n \"DEU\" : 1.\n\n# How the impact is distributed towards the impacted sectors\nproductive_capital_impact_sectoral_distrib_type: gdp\n\u003c/code\u003e\u003c/pre\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch4 class=\"heading-element\"\u003eSector scenarios\u003c/h4\u003e\u003ca id=\"user-content-sector-scenarios\" class=\"anchor\" aria-label=\"Permalink: Sector scenarios\" href=\"#sector-scenarios\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eCurrently only one sector scenario can be run per pipeline run, in the future, multiple scenario will be possible.\u003c/p\u003e\n\u003cp\u003eThe scenario is defined based on the \u003ccode\u003eexiobase3_ixi_full_sectors.csv\u003c/code\u003e file, located in the\n\u003ccode\u003econfig/mriot_base_scenarios/\u003c/code\u003e folder by default (which can be changed with the \u003ccode\u003emriot_base_config\u003c/code\u003e\nattribute in the \u003ccode\u003econfig.yaml\u003c/code\u003e file). Note that for user-friendliness this file is automatically copied\nto MRIOT-Tools sub-module data folder.\u003c/p\u003e\n\u003cp\u003eWe use EXIOBASE 3 as a \u003ccode\u003ebaseline\u003c/code\u003e, has it has the most sectors, then values for other tables are automatically computed\nby following a consistent sector mapping. The aggregation mapping used can be found\n\u003ca href=\"https://github.com/spjuhel/BoARIO-Tools/tree/main/boario_tools/data/aggregation_files/exiobase3_ixi\"\u003ehere\u003c/a\u003e.\u003c/p\u003e\n\u003cp\u003eThis \"main\" csv file should contain:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003ea first columns with all 163 sectors of EXIOBASE 3\u003c/li\u003e\n\u003cli\u003ean \u003ccode\u003eaffected\u003c/code\u003e column with 0 or 1 depending if the sector is impacted or not. Note that sectors in other MRIOTs that correspond to multiple sectors and where least one is affected, will be considered affected, which can produce inconsistencies. Refer to the aggregation file used.\u003c/li\u003e\n\u003cli\u003ea \u003ccode\u003erebuilding_factor\u003c/code\u003e column which states the contribution of the sector to the reconstruction effort (0 meaning it does not contribute). The column has to sum up to 1.0\u003c/li\u003e\n\u003cli\u003ean \u003ccode\u003einventory_size\u003c/code\u003e column with either a number of day or \"Infinity\". A number states the number of days worth, relative to production requirements, of input produced by the sector, that are aimed to be in the stocks of any industry. That is, \u003ccode\u003e90\u003c/code\u003e for \u003ccode\u003eCultivation of wheat\u003c/code\u003e means all industries \"store\" the equivalent of 90 times what they requirefrom this sector to produce for one day. \"Infinity\" means that input from this sectors are not considered as a constraint to production.\u003c/li\u003e\n\u003cli\u003ea \u003ccode\u003eproductive_capital_to_va_ratio\u003c/code\u003e column which states how much productive capital to estimate from the Value Added of the sector.\u003c/li\u003e\n\u003cli\u003ean \u003ccode\u003einventory_tau\u003c/code\u003e column which state the characteristic time to resupply inputs from this sector.\u003c/li\u003e\n\u003c/ul\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch4 class=\"heading-element\"\u003eSimulation scenarios\u003c/h4\u003e\u003ca id=\"user-content-simulation-scenarios\" class=\"anchor\" aria-label=\"Permalink: Simulation scenarios\" href=\"#simulation-scenarios\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eDefines the simulation space, which will be a Cartesian product of each possibility.\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003e\nflood_scenario: # Flood scenarios to run (needs to match a yaml file in flood_scenarios/)\n - germany21\n\nmriot: # The MRIOTs to run\n - exiobase3_ixi\n - eora26\n - euregio\n\nmriot_year: # The MRIOTs years to run\n - 2000\n - 2010\n\n# The type of aggregation to use (mostly full_sectors_full_regions is relevant,\n# the two other possibilities are to evaluate the effect of differences in sector/region typologies)\nmriot_aggreg:\n - full_sectors_full_regions\n - common_sectors_common_regions\n - common_sectors_full_regions\n\n# Required but currently unused, placeholder for future use.\nsectors_scenario:\n - default\n\n# Recovery scenarios to run\nrecovery_scenario:\n - reclin\n - reb\n\nrecovery_tau:\n - 90\n - 180\n - 365\n - 545\n - 730\n\n# Parameters used for the BoARIO model (see its documentation)\n\norder:\n - alt\n\npsi:\n - 0.5\n - 0.8\n - 0.85\n - 0.90\n - 0.95\n - 0.97\n - 1.0\n\nbase_alpha:\n - 1\n\nmax_alpha:\n - 1.25\n\ntau_alpha:\n - 1\n - 90\n - 180\n - 365\n - 730\n\n\u003c/code\u003e\u003c/pre\u003e\n", + "data_format": 2, + "description": "Sensitivity Analysis of BoARIO", + "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmp1f12dqr5/workflow/Snakefile\": InvalidPython: Black error:\n```\nCannot parse: 5:6: conda:\n```\n\n[DEBUG] In file \"/tmp/tmp1f12dqr5/workflow/Snakefile\": \n[DEBUG] In file \"/tmp/tmp1f12dqr5/workflow/rules/simulations.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp1f12dqr5/workflow/rules/treat_results.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp1f12dqr5/workflow/rules/prepare_simspace.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp1f12dqr5/workflow/rules/report.smk\": Formatted content is different from original\n[INFO] 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] 4 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "spjuhel/BoARIO-Sensitivity", + "latest_release": null, + "linting": "WorkflowError:\nFailed to open source file /home/sjuhel/Repos/BoARIO-MRIOT-Tools/workflow/Snakefile\nFileNotFoundError: [Errno 2] No such file or directory: \u0027/home/sjuhel/Repos/BoARIO-MRIOT-Tools/workflow/Snakefile\u0027\n", + "mandatory_flags": { + "desc": null, + "flags": null + }, + "report": true, + "software_stack_deployment": { + "conda": true, + "singularity": false, + "singularity+conda": false + }, + "standardized": true, + "stargazers_count": 1, + "subscribers_count": 1, + "topics": [], + "updated_at": 1723130213.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": null, + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpttdtum7p/hmgu-itg-single-point-analysis-pipeline-27c1941/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpttdtum7p/hmgu-itg-single-point-analysis-pipeline-27c1941/workflow/rules/0. read-config.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpttdtum7p/hmgu-itg-single-point-analysis-pipeline-27c1941/workflow/rules/3. cojo.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpttdtum7p/hmgu-itg-single-point-analysis-pipeline-27c1941/workflow/rules/2. single-cohort.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpttdtum7p/hmgu-itg-single-point-analysis-pipeline-27c1941/workflow/rules/1. variant-qc.smk\": Formatted content is different from original\n[INFO] 5 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "hmgu-itg/single-point-analysis-pipeline", + "latest_release": "0.0.2", + "linting": "", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 1, + "subscribers_count": 1, + "topics": [], + "updated_at": 1723112924.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": "A workflow comparing different python data viz libraries", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpxzz1e_6c/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "fxwiegand/python-data-visualization-benchmark", + "latest_release": null, + "linting": "Lints for snakefile /tmp/tmpxzz1e_6c/Snakefile:\n * Absolute path \"/\")[2].split(\" in line 51:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n\nLints for rule plot (line 26, /tmp/tmpxzz1e_6c/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule count_loc (line 67, /tmp/tmpxzz1e_6c/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n\nLints for rule plot_loc (line 101, /tmp/tmpxzz1e_6c/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule plot_benchmarks (line 127, /tmp/tmpxzz1e_6c/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule loc_types (line 154, /tmp/tmpxzz1e_6c/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule script_complexity (line 175, /tmp/tmpxzz1e_6c/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule generate_data (line 201, /tmp/tmpxzz1e_6c/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 1, + "subscribers_count": 3, + "topics": [], + "updated_at": 1725445373.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": null, + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpuat3kebz/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "cademirch/snakemake-phoenix-demo", + "latest_release": null, + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpuat3kebz/workflow/Snakefile\", line 2, in \u003cmodule\u003e\n import matplotlib.pyplot as plt\n\nModuleNotFoundError: No module named \u0027matplotlib\u0027\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 1, + "subscribers_count": 1, + "topics": [], + "updated_at": 1723083396.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": "Script for data collection", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp6j45yur4/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "UNSAT3D/XrayTIFF2h5", + "latest_release": null, + "linting": "Lints for rule sim (line 35, /tmp/tmp6j45yur4/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule exp (line 46, /tmp/tmp6j45yur4/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 1, + "subscribers_count": 1, + "topics": [], + "updated_at": 1723025854.0 + }, + { + "config_readme": "\u003cp\u003eDescribe how to configure the workflow (using config.yaml and maybe additional files).\nAll of them need to be present with example entries inside of the config folder.\u003c/p\u003e\n", + "data_format": 2, + "description": null, + "formatting": null, + "full_name": "3d-omics/hg_genotype", + "latest_release": "v1.1.4", + "linting": "Workflow defines that rule reference__recompress__genome__ is eligible for caching between workflows (use the --cache argument to enable this).\nWorkflow defines that rule reference__recompress__vcf__ is eligible for caching between workflows (use the --cache argument to enable this).\nWorkflow defines that rule reference__recompress__gtf__ is eligible for caching between workflows (use the --cache argument to enable this).\nWorkflow defines that rule align__index__ is eligible for caching between workflows (use the --cache argument to enable this).\nLints for rule align__index__ (line 1, /tmp/tmptci1no9b/3d-omics-hg_genotype-c4ccff0/workflow/rules/align/index.smk):\n * Param output_path is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule align__map__ (line 1, /tmp/tmptci1no9b/3d-omics-hg_genotype-c4ccff0/workflow/rules/align/map.smk):\n * Param index_prefix is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\n", + "mandatory_flags": { + "desc": null, + "flags": null + }, + "report": true, + "software_stack_deployment": { + "conda": true, + "singularity": false, + "singularity+conda": false + }, + "standardized": true, + "stargazers_count": 1, + "subscribers_count": 1, + "topics": [], + "updated_at": 1722958124.0 + }, { "config_readme": null, "data_format": 2, @@ -37713,278 +37985,6 @@ var data = "topics": [], "updated_at": 1721922508.0 }, - { - "config_readme": null, - "data_format": 2, - "description": "INSinPAL : Detecting Large Insertion Events in Whole Genome Sequencing Data at Palindromic Fragile Sites for Diagnostic Purposes", - "formatting": "[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\|\u0027\n[DEBUG] In file \"/tmp/tmpyjkqi307/Meetmet21-INSinPAL-d4d6e37/workflow/rules/mine_palindromes_in_genome.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyjkqi307/Meetmet21-INSinPAL-d4d6e37/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyjkqi307/Meetmet21-INSinPAL-d4d6e37/workflow/rules/add_mate_score_tags.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyjkqi307/Meetmet21-INSinPAL-d4d6e37/workflow/rules/estimate_size_annotsv.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyjkqi307/Meetmet21-INSinPAL-d4d6e37/workflow/rules/call_INS_SVs.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyjkqi307/Meetmet21-INSinPAL-d4d6e37/workflow/rules/select_interesting_INS.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyjkqi307/Meetmet21-INSinPAL-d4d6e37/workflow/rules/annotate_MEIs_sourceINS.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpyjkqi307/Meetmet21-INSinPAL-d4d6e37/workflow/rules/merge_callers.smk\": Formatted content is different from original\n[INFO] 8 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "Meetmet21/INSinPAL", - "latest_release": "v1.0.0", - "linting": "/tmp/tmpyjkqi307/Meetmet21-INSinPAL-d4d6e37/workflow/rules/mine_palindromes_in_genome.smk:137: SyntaxWarning: invalid escape sequence \u0027\\|\u0027\n/tmp/tmpyjkqi307/Meetmet21-INSinPAL-d4d6e37/workflow/rules/mine_palindromes_in_genome.smk:156: SyntaxWarning: invalid escape sequence \u0027\\|\u0027\nCreateRuleException in file /tmp/tmpyjkqi307/Meetmet21-INSinPAL-d4d6e37/workflow/Snakefile, line 157:\nThe name all is already used by another rule\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 1, - "subscribers_count": 1, - "topics": [], - "updated_at": 1723711860.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": "Snakemake workflow to perform Energy Landscape Analysis", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmppbo4u2oi/chiba-ai-med-Landscaper-56700b3/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "chiba-ai-med/Landscaper", - "latest_release": "v1.6.1", - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmppbo4u2oi/chiba-ai-med-Landscaper-56700b3/Snakefile\", line 11, in \u003cmodule\u003e\n INPUT = config[\"input\"]\n ~~~~~~^^^^^^^^^^\n\nKeyError: \u0027input\u0027\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 1, - "subscribers_count": 1, - "topics": [], - "updated_at": 1723617533.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmpzad5rp58/Snakefile\": Keyword \"input\" at line 140 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpzad5rp58/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "agma0/pypsa-za", - "latest_release": null, - "linting": "localrules directive specifies rules that are not present in the Snakefile:\n\tplot_network\n\nLints for snakefile /tmp/tmpzad5rp58/Snakefile:\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 91:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 95:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule build_inflow_per_country (line 111, /tmp/tmpzad5rp58/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule build_topology (line 142, /tmp/tmpzad5rp58/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule base_network (line 169, /tmp/tmpzad5rp58/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule add_electricity (line 264, /tmp/tmpzad5rp58/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule prepare_network (line 298, /tmp/tmpzad5rp58/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule solve_network (line 328, /tmp/tmpzad5rp58/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule plot_network_sa (line 364, /tmp/tmpzad5rp58/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 1, - "subscribers_count": 1, - "topics": [], - "updated_at": 1723498634.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": "Snakemake workflow to profile MHC-I neoepitopes with bulk tumor RNAseq data", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpwtunpk31/workflow/rules/index.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpwtunpk31/workflow/rules/alignment.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpwtunpk31/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpwtunpk31/workflow/rules/HLA_typing.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpwtunpk31/workflow/rules/base_recalibration.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpwtunpk31/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpwtunpk31/workflow/rules/pMHC.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpwtunpk31/workflow/rules/bam_cleaning.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpwtunpk31/workflow/rules/annotate_variants.smk\": Keyword \"input\" at line 15 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmpwtunpk31/workflow/rules/annotate_variants.smk\": Keyword \"shell\" at line 38 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpwtunpk31/workflow/rules/annotate_variants.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpwtunpk31/workflow/rules/quantification.smk\": Formatted content is different from original\n[INFO] 10 file(s) would be changed \ud83d\ude2c\n[INFO] 3 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", - "full_name": "danilotat/RNA-neoflow", - "latest_release": null, - "linting": null, - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 1, - "subscribers_count": 2, - "topics": [ - "bioinformatics", - "cancer-genomics", - "transcriptomics", - "immunology", - "neoepitopes" - ], - "updated_at": 1723471162.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": "Collection of scripts for benchmarking of seq2squiggle with other nanopore sequencing simulators", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpgku15z1q/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpgku15z1q/workflow/Snakefile\": Formatted content is different from original\n[INFO] 2 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "ZKI-PH-ImageAnalysis/seq2squiggle-benchmark", - "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpgku15z1q/workflow/Snakefile\", line 31, in \u003cmodule\u003e\n include: \"rules/d-melanogaster-genome-mode/benchmark.smk\"\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpgku15z1q/workflow/rules/d-melanogaster-genome-mode/input.smk\", line 5, in \u003cmodule\u003e\n HTTP = HTTPRemoteProvider()\n ^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/remote/__init__.py\", line 8, in __init__\n raise NotImplementedError(\n\nNotImplementedError: Remote providers have been replaced by Snakemake storage plugins. Please use the corresponding storage plugin instead (snakemake-storage-plugin-*).\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 1, - "subscribers_count": 0, - "topics": [], - "updated_at": 1724596451.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": "iSofOrmS annoTAtoR pipeline", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpe23jncir/workflow/rules/stringtie.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpe23jncir/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpe23jncir/workflow/rules/gtf_processing.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpe23jncir/workflow/rules/minimap2.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpe23jncir/workflow/rules/annotation.smk\": Formatted content is different from original\n[INFO] 5 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "LBGC-CFB/SOSTAR", - "latest_release": null, - "linting": "WorkflowError:\nWorkflow defines configfile ../config/config.yaml but it is not present or accessible (full checked path: /tmp/config/config.yaml).\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 1, - "subscribers_count": 1, - "topics": [ - "longread", - "rnaseq-pipeline" - ], - "updated_at": 1723450472.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": "HMMER-based microcin search using full microcin sequences and double-glycine signal region.", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpbbglp1gz/AaronFeller-Cinful_v2-5142ba7/workflow/rules/01_ORF_finding.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpbbglp1gz/AaronFeller-Cinful_v2-5142ba7/workflow/rules/03_merge_hmmsearch.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpbbglp1gz/AaronFeller-Cinful_v2-5142ba7/workflow/rules/06_clean_outputs.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpbbglp1gz/AaronFeller-Cinful_v2-5142ba7/workflow/rules/05_signal_hmm.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpbbglp1gz/AaronFeller-Cinful_v2-5142ba7/workflow/rules/04_analyze_outputs.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpbbglp1gz/AaronFeller-Cinful_v2-5142ba7/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpbbglp1gz/AaronFeller-Cinful_v2-5142ba7/workflow/rules/02_microcin_hmm.smk\": Formatted content is different from original\n[INFO] 7 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "AaronFeller/Cinful_v2", - "latest_release": "2.1", - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpbbglp1gz/AaronFeller-Cinful_v2-5142ba7/workflow/Snakefile\", line 8, in \u003cmodule\u003e\n include: \"rules/01_ORF_finding.smk\"\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpbbglp1gz/AaronFeller-Cinful_v2-5142ba7/workflow/rules/01_ORF_finding.smk\", line 10, in \u003cmodule\u003e\n # Edit the contig names in the protein fasta files\n ^^^^^^^^^^^^^^^^^^^\n\nKeyError: \u0027outdir\u0027\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 1, - "subscribers_count": 1, - "topics": [ - "antimicrobial-peptides", - "bacterial-genome-analysis", - "bioinformatics-pipeline", - "blast", - "hidden-markov-model", - "hmm", - "hmmer", - "hmmer3", - "search", - "microcin" - ], - "updated_at": 1724756094.0 - }, - { - "config_readme": "\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eWorkflow configuration\u003c/h1\u003e\u003ca id=\"user-content-workflow-configuration\" class=\"anchor\" aria-label=\"Permalink: Workflow configuration\" href=\"#workflow-configuration\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eConfiguration is done via the \u003ccode\u003econfig\u003c/code\u003e folder content.\u003c/p\u003e\n\u003cp\u003eIt requires a \u003ccode\u003econfig.yaml\u003c/code\u003e file, and at least one \u003ccode\u003eflood_scenarios/\u0026lt;flood-scenario\u0026gt;.yaml\u003c/code\u003e file and one \u003ccode\u003esimulations/\u0026lt;simulation-scenario\u0026gt;.yaml\u003c/code\u003e, which are described in following sections. The GitHub repository contains examples of such files that should be used as templates.\u003c/p\u003e\n\u003cp\u003eIt also requires a \u003ccode\u003emriot_params\u003c/code\u003e directory for the MRIOT handling sub-module for which you can find documentation \u003ca href=\"https://github.com/spjuhel/BoARIO-MRIOT-Tools\"\u003ehere\u003c/a\u003e.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003e\u003ccode\u003econfig.yaml\u003c/code\u003e\u003c/h2\u003e\u003ca id=\"user-content-configyaml\" class=\"anchor\" aria-label=\"Permalink: config.yaml\" href=\"#configyaml\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThis file governs the high-level configuration of the pipeline (i.e. paths, notably to other configurations files, experiences to run, variables to store, etc.)\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003eTesting\u003c/h3\u003e\u003ca id=\"user-content-testing\" class=\"anchor\" aria-label=\"Permalink: Testing\" href=\"#testing\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eTo enforce testing before using the pipeline the file contains a \u003ccode\u003etesting: True\u003c/code\u003e statement, which we suggest you keep and override when running the pipeline by using the \u003ccode\u003e--config testing=False\u003c/code\u003e flag when invoking snakemake.\u003c/p\u003e\n\u003cp\u003ecreate_flood_scenarios_csv.py\ncreate_simspace_csv.py\ngenerate_local_results_rst.py\ngenerate_mrio_compare.py\ngenerate_results_index_rst.py\ngenerate_results_rst.py\nplot_results.py\nprep_plot_df.py\nregroup_aggreg.py\nsimulate.py\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003eMRIOT-Tools sub-module configuration\u003c/h3\u003e\u003ca id=\"user-content-mriot-tools-sub-module-configuration\" class=\"anchor\" aria-label=\"Permalink: MRIOT-Tools sub-module configuration\" href=\"#mriot-tools-sub-module-configuration\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThis part of the configuration give the required details for the MRIOTs-Tools sub-module and essentially governs\nwhere MRIOTs data should be looked for and stored. We suggest to keep it as is in most cases.\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003eprefix\u003c/code\u003e is the sub-directory of the pipeline global output which contains everything related to the sub-module. This is where the sub-module looks for configuration files and where it store the MRIOTs data.\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003eXXX_dir\u003c/code\u003e are the sub-sub-folders where corresponding data is to be found/stored\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003ecommon_aggreg\u003c/code\u003e is the name of the aggregation common to all MRIOTs\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003emriot_base_aggreg\u003c/code\u003e is the name of the initial, not aggregated MRIOT for each table type.\u003c/li\u003e\n\u003c/ul\u003e\n\u003cpre\u003e\u003ccode\u003edata-mriot:\n prefix: \"mriot_data/\"\n downloaded_mriot_dir: \"downloaded\"\n parsed_mriot_dir: \"parsed\"\n aggregated_mriot_dir: \"parsed\"\n mriot_params_dir: \"config/mriot_params\"\n\n common_aggreg: \"common_sectors_common_regions\"\n mriot_base_aggreg:\n exiobase3_ixi : \"full_sectors_full_regions\"\n exiobase3_pxp : \"full_sectors_full_regions\"\n eora26: \"full_no_reexport_sectors_full_regions\"\n euregio: \"full_sectors_full_regions\"\n\n\u003c/code\u003e\u003c/pre\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003eScenarios files\u003c/h3\u003e\u003ca id=\"user-content-scenarios-files\" class=\"anchor\" aria-label=\"Permalink: Scenarios files\" href=\"#scenarios-files\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eNext the file should define the scenarios to run, for instance:\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003eflood scenario: flood_scenarios/germany21.yaml\nsimulation space test: simulations/test.yaml\nsimulation space: simulations/germany21.yaml\n\u003c/code\u003e\u003c/pre\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch4 class=\"heading-element\"\u003eFlood scenarios\u003c/h4\u003e\u003ca id=\"user-content-flood-scenarios\" class=\"anchor\" aria-label=\"Permalink: Flood scenarios\" href=\"#flood-scenarios\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eFlood scenarios define the direct impact for each MRIOTs. Format is the following:\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003ename: \u0026lt;name of the scenario\u0026gt;\n\nyear: \u0026lt;year of the impact\u0026gt;\nunit: \u0026lt;monetary unit\u0026gt; (\"euro\", \"dollar\", ...)\nprod_cap_impact_unit: \u0026lt;unit value of impact on productive capital\u0026gt;\nhouse_impact_unit: \u0026lt;unit value of impact on households capital\u0026gt; (Can be 0)\nestimated_gdp_unit: \u0026lt;unit value of GDP of the whole region impacted\u0026gt; Used to translate the impact in relative terms\n\nduration: \u0026lt;duration of the event\u0026gt;\n\n# name of the country affected in each of the MRIOTs\ncountries_affected:\n exiobase3_ixi: \"DE\"\n eora26: \"DEU\"\n euregio: \"DE\"\n\n# name of the regions affected in each of the MRIOTs : share of the impact\n# this is mainly for euregio where there subregions are impacted\n# should also have a \"common\" element if you wish to run simulation on\n# the aggregated version of the MRIOTs\nregions_affected:\n exiobase3_ixi:\n \"DE\": 1.\n eora26:\n \"DEU\" : 1.\n euregio:\n \u0027DE21\u0027 : 0.00137977016177574\n \u0027DE22\u0027 : 0.00137977016177574\n \u0027DE23\u0027 : 0.00137977016177574\n [...]\n common:\n \"DEU\" : 1.\n\n# How the impact is distributed towards the impacted sectors\nproductive_capital_impact_sectoral_distrib_type: gdp\n\u003c/code\u003e\u003c/pre\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch4 class=\"heading-element\"\u003eSector scenarios\u003c/h4\u003e\u003ca id=\"user-content-sector-scenarios\" class=\"anchor\" aria-label=\"Permalink: Sector scenarios\" href=\"#sector-scenarios\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eCurrently only one sector scenario can be run per pipeline run, in the future, multiple scenario will be possible.\u003c/p\u003e\n\u003cp\u003eThe scenario is defined based on the \u003ccode\u003eexiobase3_ixi_full_sectors.csv\u003c/code\u003e file, located in the\n\u003ccode\u003econfig/mriot_base_scenarios/\u003c/code\u003e folder by default (which can be changed with the \u003ccode\u003emriot_base_config\u003c/code\u003e\nattribute in the \u003ccode\u003econfig.yaml\u003c/code\u003e file). Note that for user-friendliness this file is automatically copied\nto MRIOT-Tools sub-module data folder.\u003c/p\u003e\n\u003cp\u003eWe use EXIOBASE 3 as a \u003ccode\u003ebaseline\u003c/code\u003e, has it has the most sectors, then values for other tables are automatically computed\nby following a consistent sector mapping. The aggregation mapping used can be found\n\u003ca href=\"https://github.com/spjuhel/BoARIO-Tools/tree/main/boario_tools/data/aggregation_files/exiobase3_ixi\"\u003ehere\u003c/a\u003e.\u003c/p\u003e\n\u003cp\u003eThis \"main\" csv file should contain:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003ea first columns with all 163 sectors of EXIOBASE 3\u003c/li\u003e\n\u003cli\u003ean \u003ccode\u003eaffected\u003c/code\u003e column with 0 or 1 depending if the sector is impacted or not. Note that sectors in other MRIOTs that correspond to multiple sectors and where least one is affected, will be considered affected, which can produce inconsistencies. Refer to the aggregation file used.\u003c/li\u003e\n\u003cli\u003ea \u003ccode\u003erebuilding_factor\u003c/code\u003e column which states the contribution of the sector to the reconstruction effort (0 meaning it does not contribute). The column has to sum up to 1.0\u003c/li\u003e\n\u003cli\u003ean \u003ccode\u003einventory_size\u003c/code\u003e column with either a number of day or \"Infinity\". A number states the number of days worth, relative to production requirements, of input produced by the sector, that are aimed to be in the stocks of any industry. That is, \u003ccode\u003e90\u003c/code\u003e for \u003ccode\u003eCultivation of wheat\u003c/code\u003e means all industries \"store\" the equivalent of 90 times what they requirefrom this sector to produce for one day. \"Infinity\" means that input from this sectors are not considered as a constraint to production.\u003c/li\u003e\n\u003cli\u003ea \u003ccode\u003eproductive_capital_to_va_ratio\u003c/code\u003e column which states how much productive capital to estimate from the Value Added of the sector.\u003c/li\u003e\n\u003cli\u003ean \u003ccode\u003einventory_tau\u003c/code\u003e column which state the characteristic time to resupply inputs from this sector.\u003c/li\u003e\n\u003c/ul\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch4 class=\"heading-element\"\u003eSimulation scenarios\u003c/h4\u003e\u003ca id=\"user-content-simulation-scenarios\" class=\"anchor\" aria-label=\"Permalink: Simulation scenarios\" href=\"#simulation-scenarios\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eDefines the simulation space, which will be a Cartesian product of each possibility.\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003e\nflood_scenario: # Flood scenarios to run (needs to match a yaml file in flood_scenarios/)\n - germany21\n\nmriot: # The MRIOTs to run\n - exiobase3_ixi\n - eora26\n - euregio\n\nmriot_year: # The MRIOTs years to run\n - 2000\n - 2010\n\n# The type of aggregation to use (mostly full_sectors_full_regions is relevant,\n# the two other possibilities are to evaluate the effect of differences in sector/region typologies)\nmriot_aggreg:\n - full_sectors_full_regions\n - common_sectors_common_regions\n - common_sectors_full_regions\n\n# Required but currently unused, placeholder for future use.\nsectors_scenario:\n - default\n\n# Recovery scenarios to run\nrecovery_scenario:\n - reclin\n - reb\n\nrecovery_tau:\n - 90\n - 180\n - 365\n - 545\n - 730\n\n# Parameters used for the BoARIO model (see its documentation)\n\norder:\n - alt\n\npsi:\n - 0.5\n - 0.8\n - 0.85\n - 0.90\n - 0.95\n - 0.97\n - 1.0\n\nbase_alpha:\n - 1\n\nmax_alpha:\n - 1.25\n\ntau_alpha:\n - 1\n - 90\n - 180\n - 365\n - 730\n\n\u003c/code\u003e\u003c/pre\u003e\n", - "data_format": 2, - "description": "Sensitivity Analysis of BoARIO", - "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmp1f12dqr5/workflow/Snakefile\": InvalidPython: Black error:\n```\nCannot parse: 5:6: conda:\n```\n\n[DEBUG] In file \"/tmp/tmp1f12dqr5/workflow/Snakefile\": \n[DEBUG] In file \"/tmp/tmp1f12dqr5/workflow/rules/simulations.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp1f12dqr5/workflow/rules/treat_results.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp1f12dqr5/workflow/rules/prepare_simspace.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp1f12dqr5/workflow/rules/report.smk\": Formatted content is different from original\n[INFO] 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] 4 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "spjuhel/BoARIO-Sensitivity", - "latest_release": null, - "linting": "WorkflowError:\nFailed to open source file /home/sjuhel/Repos/BoARIO-MRIOT-Tools/workflow/Snakefile\nFileNotFoundError: [Errno 2] No such file or directory: \u0027/home/sjuhel/Repos/BoARIO-MRIOT-Tools/workflow/Snakefile\u0027\n", - "mandatory_flags": { - "desc": null, - "flags": null - }, - "report": true, - "software_stack_deployment": { - "conda": true, - "singularity": false, - "singularity+conda": false - }, - "standardized": true, - "stargazers_count": 1, - "subscribers_count": 1, - "topics": [], - "updated_at": 1723130213.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpttdtum7p/hmgu-itg-single-point-analysis-pipeline-27c1941/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpttdtum7p/hmgu-itg-single-point-analysis-pipeline-27c1941/workflow/rules/0. read-config.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpttdtum7p/hmgu-itg-single-point-analysis-pipeline-27c1941/workflow/rules/3. cojo.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpttdtum7p/hmgu-itg-single-point-analysis-pipeline-27c1941/workflow/rules/2. single-cohort.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpttdtum7p/hmgu-itg-single-point-analysis-pipeline-27c1941/workflow/rules/1. variant-qc.smk\": Formatted content is different from original\n[INFO] 5 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "hmgu-itg/single-point-analysis-pipeline", - "latest_release": "0.0.2", - "linting": "", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 1, - "subscribers_count": 1, - "topics": [], - "updated_at": 1723112924.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": "A workflow comparing different python data viz libraries", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpxzz1e_6c/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "fxwiegand/python-data-visualization-benchmark", - "latest_release": null, - "linting": "Lints for snakefile /tmp/tmpxzz1e_6c/Snakefile:\n * Absolute path \"/\")[2].split(\" in line 51:\n Do not define absolute paths inside of the workflow, since this renders\n your workflow irreproducible on other machines. Use path relative to the\n working directory instead, or make the path configurable via a config\n file.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n\nLints for rule plot (line 26, /tmp/tmpxzz1e_6c/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule count_loc (line 67, /tmp/tmpxzz1e_6c/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n\nLints for rule plot_loc (line 101, /tmp/tmpxzz1e_6c/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule plot_benchmarks (line 127, /tmp/tmpxzz1e_6c/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule loc_types (line 154, /tmp/tmpxzz1e_6c/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule script_complexity (line 175, /tmp/tmpxzz1e_6c/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule generate_data (line 201, /tmp/tmpxzz1e_6c/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 1, - "subscribers_count": 3, - "topics": [], - "updated_at": 1725445373.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpuat3kebz/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "cademirch/snakemake-phoenix-demo", - "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpuat3kebz/workflow/Snakefile\", line 2, in \u003cmodule\u003e\n import matplotlib.pyplot as plt\n\nModuleNotFoundError: No module named \u0027matplotlib\u0027\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 1, - "subscribers_count": 1, - "topics": [], - "updated_at": 1723083396.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": "Script for data collection", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp6j45yur4/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "UNSAT3D/XrayTIFF2h5", - "latest_release": null, - "linting": "Lints for rule sim (line 35, /tmp/tmp6j45yur4/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule exp (line 46, /tmp/tmp6j45yur4/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 1, - "subscribers_count": 1, - "topics": [], - "updated_at": 1723025854.0 - }, - { - "config_readme": "\u003cp\u003eDescribe how to configure the workflow (using config.yaml and maybe additional files).\nAll of them need to be present with example entries inside of the config folder.\u003c/p\u003e\n", - "data_format": 2, - "description": null, - "formatting": null, - "full_name": "3d-omics/hg_genotype", - "latest_release": "v1.1.4", - "linting": "Workflow defines that rule reference__recompress__genome__ is eligible for caching between workflows (use the --cache argument to enable this).\nWorkflow defines that rule reference__recompress__vcf__ is eligible for caching between workflows (use the --cache argument to enable this).\nWorkflow defines that rule reference__recompress__gtf__ is eligible for caching between workflows (use the --cache argument to enable this).\nWorkflow defines that rule align__index__ is eligible for caching between workflows (use the --cache argument to enable this).\nLints for rule align__index__ (line 1, /tmp/tmptci1no9b/3d-omics-hg_genotype-c4ccff0/workflow/rules/align/index.smk):\n * Param output_path is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule align__map__ (line 1, /tmp/tmptci1no9b/3d-omics-hg_genotype-c4ccff0/workflow/rules/align/map.smk):\n * Param index_prefix is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\n", - "mandatory_flags": { - "desc": null, - "flags": null - }, - "report": true, - "software_stack_deployment": { - "conda": true, - "singularity": false, - "singularity+conda": false - }, - "standardized": true, - "stargazers_count": 1, - "subscribers_count": 1, - "topics": [], - "updated_at": 1722958124.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": "Workflow for merging multi-lane fastq files from the Illumina NextSeq 550 using Snakemake. In addition, basic QC and md5 checksums are generated.", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmplqdsifer/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "GenoMixer/illumina-snakemake-nextseq-pipeline", - "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmplqdsifer/Snakefile\", line 19, in \u003cmodule\u003e\n samples=pd.read_csv(\"SampleSheet.csv\",skiprows=16).set_index(\"Sample_ID\")\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1026, in read_csv\n return _read(filepath_or_buffer, kwds)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 620, in _read\n parser = TextFileReader(filepath_or_buffer, **kwds)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1620, in __init__\n self._engine = self._make_engine(f, self.engine)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/parsers/readers.py\", line 1880, in _make_engine\n self.handles = get_handle(\n ^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pandas/io/common.py\", line 873, in get_handle\n handle = open(\n ^^^^^\n\nFileNotFoundError: [Errno 2] No such file or directory: \u0027SampleSheet.csv\u0027\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 1, - "subscribers_count": 1, - "topics": [], - "updated_at": 1723712151.0 - }, { "config_readme": null, "data_format": 2, @@ -43575,6 +43575,74 @@ var data = "topics": [], "updated_at": 1551028733.0 }, + { + "config_readme": null, + "data_format": 2, + "description": "Pipeline to process sequencing reads from a ChIP-DIP experiment", + "formatting": "[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\.\u0027\n[DEBUG] In file \"/tmp/tmp98azcfmj/GuttmanLab-chipdip-pipeline-6400934/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "GuttmanLab/chipdip-pipeline", + "latest_release": "v0.9_journal_submission", + "linting": "/tmp/tmp98azcfmj/GuttmanLab-chipdip-pipeline-6400934/Snakefile:353: SyntaxWarning: invalid escape sequence \u0027\\.\u0027\n output:\nUsing BarcodeID config: example_config.txt\nUsing split-pool format file: example_format.txt\nUsing 7 tags\nUsing mm10\nUsing samples file: example_samples.json\nAll data will be written to: \nUsing temporary directory: /central/scratch/\nWill generate bam files for individual targets using:\n\t min_oligos: 2\n\t proportion: 0.8\n\t max_size: 10000\nUsing cutadapt sequence file -g file:assets/dpm96.fasta\nUsing bead oligo file -g file:assets/bpm.fasta\nOutput logs path created: True\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp98azcfmj/GuttmanLab-chipdip-pipeline-6400934/Snakefile\", line 193, in \u003cmodule\u003e\n\nNameError: name \u0027json\u0027 is not defined. Did you forget to import \u0027json\u0027\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 2, + "subscribers_count": 6, + "topics": [], + "updated_at": 1723526284.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": "Pipeline for decoding the functional networks of non-model organisms", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp4s_gu92o/samsledje-philharmonic-04b1537/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "samsledje/philharmonic", + "latest_release": "v0.1.0", + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp4s_gu92o/samsledje-philharmonic-04b1537/Snakefile\", line 426, in \u003cmodule\u003e\n\n File \"\u003cfrozen os\u003e\", line 714, in __getitem__\n\nKeyError: \u0027OPENAI_API_KEY\u0027\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 2, + "subscribers_count": 1, + "topics": [], + "updated_at": 1723468674.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": null, + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpxvnjzm_m/workflow/rules/QualityControl.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpxvnjzm_m/workflow/rules/reference.smk\": Keyword \"output\" at line 26 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpxvnjzm_m/workflow/rules/reference.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpxvnjzm_m/workflow/rules/extract_signals.smk\": Keyword \"input\" at line 47 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmpxvnjzm_m/workflow/rules/extract_signals.smk\": Keyword \"input\" at line 92 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpxvnjzm_m/workflow/rules/extract_signals.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpxvnjzm_m/workflow/rules/filtering.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpxvnjzm_m/workflow/rules/trimming.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpxvnjzm_m/workflow/rules/bam_to_fastq.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpxvnjzm_m/workflow/rules/ichorCNA.smk\": Formatted content is different from original\n[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\.\u0027\n[DEBUG] In file \"/tmp/tmpxvnjzm_m/workflow/rules/GC_bias.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpxvnjzm_m/workflow/rules/common.smk\": Formatted content is different from original\n[INFO] 9 file(s) would be changed \ud83d\ude2c\n[INFO] 2 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", + "full_name": "brmprnk/cfDNA-UniFlow", + "latest_release": null, + "linting": "WorkflowError:\nWorkflow defines configfile config/config.yaml but it is not present or accessible (full checked path: /tmp/tmpxvnjzm_m/config/config.yaml).\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 2, + "subscribers_count": 1, + "topics": [], + "updated_at": 1723729329.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": "Price Formation in 100% Variable Renewable Energy Systems", + "formatting": null, + "full_name": "fneum/price-formation", + "latest_release": "v0.1.0", + "linting": "WorkflowError:\nNo storage provider found for query https://researchdata.reading.ac.uk/321/4/ERA5_data_1950-2020.zip. Either install the required storage plugin or check your query. Also consider to explicitly specify the storage provider to get a more informative error message.\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 2, + "subscribers_count": 4, + "topics": [], + "updated_at": 1723381193.0 + }, { "config_readme": "\u003cp\u003eDescribe how to configure the workflow (using config.yaml and maybe additional files).\nAll of them need to be present with example entries inside of the config folder.\u003c/p\u003e\n", "data_format": 2, @@ -44382,74 +44450,6 @@ var data = "topics": [], "updated_at": 1722291218.0 }, - { - "config_readme": null, - "data_format": 2, - "description": "Pipeline to process sequencing reads from a ChIP-DIP experiment", - "formatting": "[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\.\u0027\n[DEBUG] In file \"/tmp/tmp98azcfmj/GuttmanLab-chipdip-pipeline-6400934/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "GuttmanLab/chipdip-pipeline", - "latest_release": "v0.9_journal_submission", - "linting": "/tmp/tmp98azcfmj/GuttmanLab-chipdip-pipeline-6400934/Snakefile:353: SyntaxWarning: invalid escape sequence \u0027\\.\u0027\n output:\nUsing BarcodeID config: example_config.txt\nUsing split-pool format file: example_format.txt\nUsing 7 tags\nUsing mm10\nUsing samples file: example_samples.json\nAll data will be written to: \nUsing temporary directory: /central/scratch/\nWill generate bam files for individual targets using:\n\t min_oligos: 2\n\t proportion: 0.8\n\t max_size: 10000\nUsing cutadapt sequence file -g file:assets/dpm96.fasta\nUsing bead oligo file -g file:assets/bpm.fasta\nOutput logs path created: True\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp98azcfmj/GuttmanLab-chipdip-pipeline-6400934/Snakefile\", line 193, in \u003cmodule\u003e\n\nNameError: name \u0027json\u0027 is not defined. Did you forget to import \u0027json\u0027\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 2, - "subscribers_count": 6, - "topics": [], - "updated_at": 1723526284.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": "Pipeline for decoding the functional networks of non-model organisms", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp4s_gu92o/samsledje-philharmonic-04b1537/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "samsledje/philharmonic", - "latest_release": "v0.1.0", - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp4s_gu92o/samsledje-philharmonic-04b1537/Snakefile\", line 426, in \u003cmodule\u003e\n\n File \"\u003cfrozen os\u003e\", line 714, in __getitem__\n\nKeyError: \u0027OPENAI_API_KEY\u0027\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 2, - "subscribers_count": 1, - "topics": [], - "updated_at": 1723468674.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpxvnjzm_m/workflow/rules/QualityControl.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpxvnjzm_m/workflow/rules/reference.smk\": Keyword \"output\" at line 26 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpxvnjzm_m/workflow/rules/reference.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpxvnjzm_m/workflow/rules/extract_signals.smk\": Keyword \"input\" at line 47 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmpxvnjzm_m/workflow/rules/extract_signals.smk\": Keyword \"input\" at line 92 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpxvnjzm_m/workflow/rules/extract_signals.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpxvnjzm_m/workflow/rules/filtering.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpxvnjzm_m/workflow/rules/trimming.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmpxvnjzm_m/workflow/rules/bam_to_fastq.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpxvnjzm_m/workflow/rules/ichorCNA.smk\": Formatted content is different from original\n[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\.\u0027\n[DEBUG] In file \"/tmp/tmpxvnjzm_m/workflow/rules/GC_bias.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpxvnjzm_m/workflow/rules/common.smk\": Formatted content is different from original\n[INFO] 9 file(s) would be changed \ud83d\ude2c\n[INFO] 2 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", - "full_name": "brmprnk/cfDNA-UniFlow", - "latest_release": null, - "linting": "WorkflowError:\nWorkflow defines configfile config/config.yaml but it is not present or accessible (full checked path: /tmp/tmpxvnjzm_m/config/config.yaml).\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 2, - "subscribers_count": 1, - "topics": [], - "updated_at": 1723729329.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": "Price Formation in 100% Variable Renewable Energy Systems", - "formatting": null, - "full_name": "fneum/price-formation", - "latest_release": "v0.1.0", - "linting": "WorkflowError:\nNo storage provider found for query https://researchdata.reading.ac.uk/321/4/ERA5_data_1950-2020.zip. Either install the required storage plugin or check your query. Also consider to explicitly specify the storage provider to get a more informative error message.\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 2, - "subscribers_count": 4, - "topics": [], - "updated_at": 1723381193.0 - }, { "config_readme": null, "data_format": 2, @@ -47143,6 +47143,29 @@ var data = ], "updated_at": 1617804426.0 }, + { + "config_readme": null, + "data_format": 2, + "description": "Materials for Tech-Talk: Workflows as part of reproducible and replicable science", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpt3_p426q/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "mja/tech-talk-workflows", + "latest_release": null, + "linting": "Lints for rule render (line 1, /tmp/tmpt3_p426q/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule lv (line 19, /tmp/tmpt3_p426q/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule simu (line 34, /tmp/tmpt3_p426q/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule pca (line 64, /tmp/tmpt3_p426q/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 3, + "subscribers_count": 1, + "topics": [ + "data-science", + "nextflow", + "reproducible-research", + "snakemake", + "workflow" + ], + "updated_at": 1723737700.0 + }, { "config_readme": null, "data_format": 2, @@ -47603,29 +47626,6 @@ var data = "topics": [], "updated_at": 1722953617.0 }, - { - "config_readme": null, - "data_format": 2, - "description": "Materials for Tech-Talk: Workflows as part of reproducible and replicable science", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpt3_p426q/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "mja/tech-talk-workflows", - "latest_release": null, - "linting": "Lints for rule render (line 1, /tmp/tmpt3_p426q/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule lv (line 19, /tmp/tmpt3_p426q/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule simu (line 34, /tmp/tmpt3_p426q/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule pca (line 64, /tmp/tmpt3_p426q/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 3, - "subscribers_count": 1, - "topics": [ - "data-science", - "nextflow", - "reproducible-research", - "snakemake", - "workflow" - ], - "updated_at": 1723737700.0 - }, { "config_readme": null, "data_format": 2, @@ -49224,324 +49224,6 @@ var data = "topics": [], "updated_at": 1616871931.0 }, - { - "config_readme": null, - "data_format": 2, - "description": null, - "formatting": null, - "full_name": "Arcadia-Science/2024-Ecoli-amr-genotype-phenotype_7000strains", - "latest_release": "v1.0", - "linting": "Lints for rule create_file (line 6, /tmp/tmpc1lvu2e1/Arcadia-Science-2024-Ecoli-amr-genotype-phenotype_7000strains-21aa07e/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 4, - "subscribers_count": 2, - "topics": [], - "updated_at": 1726614952.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp0odzv2xt/marschall-lab-strand-seq-graph-phasing-95e6472/workflow/rules/strandseq_breakpoints.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp0odzv2xt/marschall-lab-strand-seq-graph-phasing-95e6472/workflow/rules/sample_table.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp0odzv2xt/marschall-lab-strand-seq-graph-phasing-95e6472/workflow/rules/evaluate.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp0odzv2xt/marschall-lab-strand-seq-graph-phasing-95e6472/workflow/rules/collect_output.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp0odzv2xt/marschall-lab-strand-seq-graph-phasing-95e6472/workflow/rules/align_to_reference.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp0odzv2xt/marschall-lab-strand-seq-graph-phasing-95e6472/workflow/Snakefile\": Formatted content is different from original\n[INFO] 6 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "marschall-lab/strand-seq-graph-phasing", - "latest_release": "v0.5.01", - "linting": "KeyError in file /tmp/tmp0odzv2xt/marschall-lab-strand-seq-graph-phasing-95e6472/workflow/Snakefile, line 11:\n\u0027segmentLengthThreshold\u0027\n File \"/tmp/tmp0odzv2xt/marschall-lab-strand-seq-graph-phasing-95e6472/workflow/Snakefile\", line 11, in \u003cmodule\u003e\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 4, - "subscribers_count": 2, - "topics": [], - "updated_at": 1726760797.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": "MAGqual is a command line tool to evaluate the quality of metagenomic bins and generate recommended metadata in line with the MIMAG standards ", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpiawki_65/ac1513-MAGqual-14e7706/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "ac1513/MAGqual", - "latest_release": "v.0.3.0", - "linting": "Lints for snakefile /tmp/tmpiawki_65/ac1513-MAGqual-14e7706/workflow/Snakefile:\n * Path composition with \u0027+\u0027 in line 19:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule bakta_db (line 51, /tmp/tmpiawki_65/ac1513-MAGqual-14e7706/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Shell command directly uses variable JOBID from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule bakta (line 109, /tmp/tmpiawki_65/ac1513-MAGqual-14e7706/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param database is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule checkm_db (line 160, /tmp/tmpiawki_65/ac1513-MAGqual-14e7706/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Shell command directly uses variable JOBID from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule checkm (line 216, /tmp/tmpiawki_65/ac1513-MAGqual-14e7706/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Shell command directly uses variable ext from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Param database is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule seqkit (line 272, /tmp/tmpiawki_65/ac1513-MAGqual-14e7706/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule high_mags (line 308, /tmp/tmpiawki_65/ac1513-MAGqual-14e7706/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Shell command directly uses variable ext from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Param out_loc is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule report_gen (line 361, /tmp/tmpiawki_65/ac1513-MAGqual-14e7706/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Shell command directly uses variable JOBID from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 4, - "subscribers_count": 1, - "topics": [ - "metagenomic-analysis", - "metagenomic-pipeline", - "metagenomics", - "snakemake", - "snakemake-pipeline" - ], - "updated_at": 1724849292.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpa7c4q4jc/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "MetaSUB-CAMP/camp_short-read-quality-control", - "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpa7c4q4jc/workflow/Snakefile\", line 14, in \u003cmodule\u003e\n dirs = Workflow_Dirs(config[\u0027work_dir\u0027], \u0027short_read_qc\u0027)\n ^^^^^^^^^^^^^^^^^^^^^\n\nKeyError: \u0027work_dir\u0027\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 4, - "subscribers_count": 3, - "topics": [], - "updated_at": 1724523776.0 - }, - { - "config_readme": "\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eConfiguration\u003c/h2\u003e\u003ca id=\"user-content-configuration\" class=\"anchor\" aria-label=\"Permalink: Configuration\" href=\"#configuration\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003einput_dir\u003c/code\u003e : Path to the input folder, containing fastq files in compressed or decompressed format. The pipeline expects the input files to conform to 1 of 2 directory structures.\n1: \u003ccode\u003einput_dir\u003c/code\u003e contains subfolders for each sampleID/barcode, if that is the case all fastq files in each subfolder are concatenated and the subfolder name is used as a sample ID downstream. This is usually the \"fastq_pass\" folder from nanopore sequencing and basecalling output (atleast when using Guppy).\n2: \u003ccode\u003einput_dir\u003c/code\u003e contains already concatenated fastq files, directly located in \u003ccode\u003einput_dir\u003c/code\u003e. If that is the case, the pipeline uses the entire filename as a sample ID downstream. This is usually the case output from Dorado re-basecalling with demultiplexing enabled.\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003eoutput_dir\u003c/code\u003e: Output directory with the final results and a few intermediary files, that can be used for other downstream purposes if desired.\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003etmp_dir\u003c/code\u003e: Directory for temporary files.\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003elog_dir\u003c/code\u003e: Directory for log files for all invoked rules.\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003edb_path_sintax\u003c/code\u003e: Database to infer taxonomy using the SINTAX algorithm. Contains sequenceID, taxonomy string and fasta sequence.\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003edb_path_blast\u003c/code\u003e: Nucleotide blast formatted database to infer taxonomy using BLASTn algorithm.\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003eevalue\u003c/code\u003e: E-value cutoff for blast. Default = 1e-10.\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003elength_lower_limit\u003c/code\u003e: Argument passed on to \u003ccode\u003echopper\u003c/code\u003e for filtering reads. Appropriate values depends on amplicon length. This can be checked by running the helper script scripts/nanoplot.sh\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003elength_upper_limit\u003c/code\u003e: Argument passed on to \u003ccode\u003echopper\u003c/code\u003e for filtering reads. Appropriate values depends on amplicon length. This can be checked by running the helper script scripts/nanoplot.sh\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003equality_cut_off\u003c/code\u003e: Argument passed on to \u003ccode\u003echopper\u003c/code\u003e for filtering reads. Appropriate value depends on the quality of your sequencing data. This can be checked by running the helper script scripts/nanoplot.sh. It is recommended to pick a Q-score \u0026gt;20, if your data permits it.\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003emax_threads\u003c/code\u003e: Maximum number of threads that can be used for any rule.\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003einclude_blast_output\u003c/code\u003e: Default = True. If true snakemake will output a final OTU-table with taxonomy infered from a blastn search against a nt blast database.\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003einclude_sintax_output\u003c/code\u003e: Default = True. If true snakemake will output a final OTU-table with taxonomy infered from a sintax formatted database.\u003c/li\u003e\n\u003c/ul\u003e\n", - "data_format": 2, - "description": "Snakemake workflow to generate OTU tables from barcoded ONT data", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp3krq9hg_/MathiasEskildsen-ONT-AmpSeq-a883884/workflow/rules/09-fix_otu_table.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp3krq9hg_/MathiasEskildsen-ONT-AmpSeq-a883884/workflow/rules/13-ampvis2_std_plots.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp3krq9hg_/MathiasEskildsen-ONT-AmpSeq-a883884/workflow/rules/06-relabel.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp3krq9hg_/MathiasEskildsen-ONT-AmpSeq-a883884/workflow/rules/08-taxonomy.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp3krq9hg_/MathiasEskildsen-ONT-AmpSeq-a883884/workflow/rules/02-filtering.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp3krq9hg_/MathiasEskildsen-ONT-AmpSeq-a883884/workflow/rules/07-clustering_identity.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp3krq9hg_/MathiasEskildsen-ONT-AmpSeq-a883884/workflow/rules/04-mapping.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp3krq9hg_/MathiasEskildsen-ONT-AmpSeq-a883884/workflow/rules/capture_config.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp3krq9hg_/MathiasEskildsen-ONT-AmpSeq-a883884/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp3krq9hg_/MathiasEskildsen-ONT-AmpSeq-a883884/workflow/rules/12-phyloseq_abund_blast.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp3krq9hg_/MathiasEskildsen-ONT-AmpSeq-a883884/workflow/rules/10-prep_for_ampvis2.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp3krq9hg_/MathiasEskildsen-ONT-AmpSeq-a883884/workflow/rules/03-clustering.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp3krq9hg_/MathiasEskildsen-ONT-AmpSeq-a883884/workflow/rules/11-prep_for_phyloseq.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp3krq9hg_/MathiasEskildsen-ONT-AmpSeq-a883884/workflow/rules/01-concatenate_fastq.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp3krq9hg_/MathiasEskildsen-ONT-AmpSeq-a883884/workflow/rules/05-polish_racon.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp3krq9hg_/MathiasEskildsen-ONT-AmpSeq-a883884/workflow/Snakefile\": Formatted content is different from original\n[INFO] 16 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "MathiasEskildsen/ONT-AmpSeq", - "latest_release": "v1.1.1", - "linting": null, - "mandatory_flags": null, - "report": true, - "software_stack_deployment": { - "conda": true - }, - "standardized": true, - "stargazers_count": 4, - "subscribers_count": 1, - "topics": [], - "updated_at": 1725438827.0 - }, - { - "config_readme": "\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eCNVand Configuration Instructions\u003c/h1\u003e\u003ca id=\"user-content-cnvand-configuration-instructions\" class=\"anchor\" aria-label=\"Permalink: CNVand Configuration Instructions\" href=\"#cnvand-configuration-instructions\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eConfiguration File\u003c/h2\u003e\u003ca id=\"user-content-configuration-file\" class=\"anchor\" aria-label=\"Permalink: Configuration File\" href=\"#configuration-file\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThe configuration file (\u003ccode\u003econfig/config.yaml\u003c/code\u003e) contains various settings that the CNVand pipeline requires. Below is an example of a typical configuration file along with an explanation of each parameter.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003eExample Configuration File\u003c/h3\u003e\u003ca id=\"user-content-example-configuration-file\" class=\"anchor\" aria-label=\"Permalink: Example Configuration File\" href=\"#example-configuration-file\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cdiv class=\"highlight highlight-source-yaml\"\u003e\u003cpre\u003e\u003cspan class=\"pl-c\"\u003e\u003cspan class=\"pl-c\"\u003e#\u003c/span\u003e## Samplesheet\u003c/span\u003e\n\u003cspan class=\"pl-ent\"\u003esamples\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003econfig/samplesheet.tsv\u003c/span\u003e\n\n\u003cspan class=\"pl-c\"\u003e\u003cspan class=\"pl-c\"\u003e#\u003c/span\u003e## Output directory\u003c/span\u003e\n\u003cspan class=\"pl-ent\"\u003eoutdir\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003eoutput/\u003c/span\u003e\n\n\u003cspan class=\"pl-c\"\u003e\u003cspan class=\"pl-c\"\u003e#\u003c/span\u003e## Reference data\u003c/span\u003e\n\u003cspan class=\"pl-ent\"\u003eref\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003egenome\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003eworkflow/resources/Homo_sapiens_assembly38.fasta \u003c/span\u003e\u003cspan class=\"pl-c\"\u003e\u003cspan class=\"pl-c\"\u003e#\u003c/span\u003e Take care you\u0027re using the same reference in your full workflow\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003etarget_bed\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e.tests/integration/input/target.bed\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003eantitarget_bed\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e.tests/integration/input/antitarget.bed\u003c/span\u003e\n\n\u003cspan class=\"pl-c\"\u003e\u003cspan class=\"pl-c\"\u003e#\u003c/span\u003e## Toolkit parameter settings\u003c/span\u003e\n\u003cspan class=\"pl-ent\"\u003eparams\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003ecnvkit\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003etarget_coverage\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003eextra\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e-q 20\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003eantitarget_coverage\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003eextra\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e-q 20\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003ereference\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003eextra\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003ecall\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003eploidy\u003c/span\u003e: \u003cspan class=\"pl-c1\"\u003e2\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003eextra\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e \n \u003cspan class=\"pl-ent\"\u003ebintest\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003eextra\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e \n \u003cspan class=\"pl-ent\"\u003ebreaks\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003eextra\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e \n \u003cspan class=\"pl-ent\"\u003egenemetrics\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003eextra\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e \n \u003cspan class=\"pl-ent\"\u003escatter\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003ey_min\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e-2.5\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003eextra\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e \n \u003cspan class=\"pl-ent\"\u003eexport_vcf\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003eextra\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e \n \u003cspan class=\"pl-ent\"\u003esegment\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003eextra\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003eannotsv\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003eannotations\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003eworkflow/data/annotations/\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e \u003cspan class=\"pl-c\"\u003e\u003cspan class=\"pl-c\"\u003e#\u003c/span\u003e Annotations to be downloaded externally - see README.md for more details\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003eextra\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003eParameter Explanations\u003c/h3\u003e\u003ca id=\"user-content-parameter-explanations\" class=\"anchor\" aria-label=\"Permalink: Parameter Explanations\" href=\"#parameter-explanations\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch4 class=\"heading-element\"\u003eSamplesheet\u003c/h4\u003e\u003ca id=\"user-content-samplesheet\" class=\"anchor\" aria-label=\"Permalink: Samplesheet\" href=\"#samplesheet\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003cstrong\u003esamples\u003c/strong\u003e: Path to the samplesheet file that contains information about the samples to be processed. This should be set to \u003ccode\u003econfig/samplesheet.tsv\u003c/code\u003e.\u003c/li\u003e\n\u003c/ul\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch4 class=\"heading-element\"\u003eOutput Directory\u003c/h4\u003e\u003ca id=\"user-content-output-directory\" class=\"anchor\" aria-label=\"Permalink: Output Directory\" href=\"#output-directory\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003cstrong\u003eoutdir\u003c/strong\u003e: Path to the directory where the output files will be stored. This is set to \u003ccode\u003eoutput/\u003c/code\u003e.\u003c/li\u003e\n\u003c/ul\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch4 class=\"heading-element\"\u003eReference Data\u003c/h4\u003e\u003ca id=\"user-content-reference-data\" class=\"anchor\" aria-label=\"Permalink: Reference Data\" href=\"#reference-data\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003cstrong\u003eref\u003c/strong\u003e:\n\u003cul\u003e\n\u003cli\u003e\n\u003cstrong\u003egenome\u003c/strong\u003e: Path to the reference genome file. Ensure that the reference genome used here is consistent throughout your workflow. Example: \u003ccode\u003eworkflow/resources/Homo_sapiens_assembly38.fasta\u003c/code\u003e.\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003etarget_bed\u003c/strong\u003e: Path to the target BED file. Example: \u003ccode\u003e.tests/integration/input/target.bed\u003c/code\u003e.\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003eantitarget_bed\u003c/strong\u003e: Path to the antitarget BED file. Example: \u003ccode\u003e.tests/integration/input/antitarget.bed\u003c/code\u003e.\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch4 class=\"heading-element\"\u003eToolkit Parameter Settings\u003c/h4\u003e\u003ca id=\"user-content-toolkit-parameter-settings\" class=\"anchor\" aria-label=\"Permalink: Toolkit Parameter Settings\" href=\"#toolkit-parameter-settings\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003cstrong\u003eparams\u003c/strong\u003e:\n\u003cul\u003e\n\u003cli\u003e\n\u003cstrong\u003ecnvkit\u003c/strong\u003e: Parameters for CNVkit tools.\n\u003cul\u003e\n\u003cli\u003e\n\u003cstrong\u003etarget_coverage\u003c/strong\u003e: Additional parameters for target coverage calculations. Example: \u003ccode\u003e-q 20\u003c/code\u003e.\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003eantitarget_coverage\u003c/strong\u003e: Additional parameters for antitarget coverage calculations. Example: \u003ccode\u003e-q 20\u003c/code\u003e.\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003ereference\u003c/strong\u003e: Additional parameters for reference generation.\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003ecall\u003c/strong\u003e: Parameters for CNV calling.\n\u003cul\u003e\n\u003cli\u003e\n\u003cstrong\u003eploidy\u003c/strong\u003e: Ploidy level to be used. Example: \u003ccode\u003e2\u003c/code\u003e.\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003eextra\u003c/strong\u003e: Additional parameters for the call step.\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003ebintest\u003c/strong\u003e: Additional parameters for bin testing.\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003ebreaks\u003c/strong\u003e: Additional parameters for breakpoints detection.\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003egenemetrics\u003c/strong\u003e: Additional parameters for gene metrics calculation.\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003escatter\u003c/strong\u003e: Parameters for scatter plot generation.\n\u003cul\u003e\n\u003cli\u003e\n\u003cstrong\u003ey_min\u003c/strong\u003e: Minimum y-axis value for scatter plots. Example: \u003ccode\u003e-2.5\u003c/code\u003e.\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003eextra\u003c/strong\u003e: Additional parameters for scatter plots.\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003eexport_vcf\u003c/strong\u003e: Additional parameters for VCF export.\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003esegment\u003c/strong\u003e: Additional parameters for segmentation.\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003eannotsv\u003c/strong\u003e: Parameters for AnnotSV tool.\n\u003cul\u003e\n\u003cli\u003e\n\u003cstrong\u003eannotations\u003c/strong\u003e: Path to the directory containing annotation files. Example: \u003ccode\u003eworkflow/data/annotations/\u003c/code\u003e.\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003eextra\u003c/strong\u003e: Additional parameters for AnnotSV.\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eSamplesheet\u003c/h2\u003e\u003ca id=\"user-content-samplesheet-1\" class=\"anchor\" aria-label=\"Permalink: Samplesheet\" href=\"#samplesheet-1\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThe samplesheet (\u003ccode\u003econfig/samplesheet.tsv\u003c/code\u003e) contains information about the samples to be processed by the CNVand pipeline. It includes the sample name, path to the BAM file, and path to the VCF file.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003eExample Samplesheet\u003c/h3\u003e\u003ca id=\"user-content-example-samplesheet\" class=\"anchor\" aria-label=\"Permalink: Example Samplesheet\" href=\"#example-samplesheet\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cdiv class=\"highlight highlight-source-generic-db\"\u003e\u003cpre\u003e\u003cspan class=\"pl-c1\"\u003esample bam_path vcf_path\u003c/span\u003e\n\u003cspan class=\"pl-c1\"\u003eM24352 .tests/integration/input/M24352_CHR21.bam .tests/integration/input/M24352_CHR21.vcf.gz\u003c/span\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003eColumn Explanations\u003c/h3\u003e\u003ca id=\"user-content-column-explanations\" class=\"anchor\" aria-label=\"Permalink: Column Explanations\" href=\"#column-explanations\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003cstrong\u003esample\u003c/strong\u003e: Unique identifier for the sample. Example: \u003ccode\u003eM24352\u003c/code\u003e.\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003ebam_path\u003c/strong\u003e: Path to the BAM file for the sample. Example: \u003ccode\u003e.tests/integration/input/M24352_CHR21.bam\u003c/code\u003e.\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003evcf_path\u003c/strong\u003e: Path to the VCF file for the sample. Example: \u003ccode\u003e.tests/integration/input/M24352_CHR21.vcf.gz\u003c/code\u003e.\u003c/li\u003e\n\u003c/ul\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eSummary\u003c/h2\u003e\u003ca id=\"user-content-summary\" class=\"anchor\" aria-label=\"Permalink: Summary\" href=\"#summary\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003col\u003e\n\u003cli\u003e\n\u003cstrong\u003eConfiguration File\u003c/strong\u003e: Ensure all paths and parameters are correctly set in the \u003ccode\u003econfig/config.yaml\u003c/code\u003e file.\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003eSamplesheet\u003c/strong\u003e: Ensure the \u003ccode\u003econfig/samplesheet.tsv\u003c/code\u003e file contains accurate paths to the BAM and VCF files for each sample.\u003c/li\u003e\n\u003c/ol\u003e\n\u003cp\u003eBy following these instructions, you will set up the CNVand pipeline correctly, ensuring accurate CNV analysis and annotation.\u003c/p\u003e\n", - "data_format": 2, - "description": "A snakemake workflow to analyse and annotate copy number variants", - "formatting": null, - "full_name": "IHGGM-Aachen/CNVand", - "latest_release": "0.3", - "linting": null, - "mandatory_flags": null, - "report": true, - "software_stack_deployment": { - "conda": true, - "singularity": false, - "singularity+conda": false - }, - "standardized": true, - "stargazers_count": 4, - "subscribers_count": 1, - "topics": [], - "updated_at": 1725145635.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": "A snakemake workflow based on the obitools suite of programs, that analyzes DNA metabarcoding data.", - "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmpap8ndjen/AnneSoBen-obitools_workflow-82f5ec5/workflow/Snakefile\": TabError: inconsistent use of tabs and spaces in indentation (\u003cstring\u003e, line 209)\n[INFO] In file \"/tmp/tmpap8ndjen/AnneSoBen-obitools_workflow-82f5ec5/workflow/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n\nsnakefmt version: 0.10.2", - "full_name": "AnneSoBen/obitools_workflow", - "latest_release": "v1.0.2", - "linting": "TabError in file \u003cstring\u003e, line 209:\ninconsistent use of tabs and spaces in indentation:\n\t\tuniq=folder_prefix+\"uniq\"\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/tokenize.py\", line 580, in _generate_tokens_from_c_tokenizer\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/tokenize.py\", line 576, in _generate_tokens_from_c_tokenizer\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 4, - "subscribers_count": 2, - "topics": [ - "edna", - "metabarcoding", - "bioinformatics-pipeline", - "edna-pipeline" - ], - "updated_at": 1725781796.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": "Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2", - "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmp9156cwzx/Snakefile\": Keyword \"input\" at line 98 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmp9156cwzx/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "blab/cartography", - "latest_release": null, - "linting": "/tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile:808: SyntaxWarning: invalid escape sequence \u0027\\-\u0027\n rule seasonal_flu_training_concat_scatterplot_table:\n/tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile:818: SyntaxWarning: invalid escape sequence \u0027\\-\u0027\n column = \"pearson_coef\",\n/tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile:1180: SyntaxWarning: invalid escape sequence \u0027\\-\u0027\n \n/tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile:1190: SyntaxWarning: invalid escape sequence \u0027\\-\u0027\n shell:\n/tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile:2752: SyntaxWarning: invalid escape sequence \u0027\\-\u0027\n/tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile:2761: SyntaxWarning: invalid escape sequence \u0027\\-\u0027\n/tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile:2813: SyntaxWarning: invalid escape sequence \u0027\\-\u0027\n/tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile:2821: SyntaxWarning: invalid escape sequence \u0027\\-\u0027\n/tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile:2842: SyntaxWarning: invalid escape sequence \u0027\\-\u0027\n/tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile:2850: SyntaxWarning: invalid escape sequence \u0027\\-\u0027\nLints for snakefile /tmp/tmp9156cwzx/simulations/Snakefile:\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n\nLints for snakefile /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile:\n * Path composition with \u0027+\u0027 in line 899:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile:\n * Path composition with \u0027+\u0027 in line 1160:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile:\n * Path composition with \u0027+\u0027 in line 808:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile:\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n\nLints for snakefile /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile:\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n\nLints for rule simulations_run_simulation (line 36, /tmp/tmp9156cwzx/simulations/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Shell command directly uses variable SNAKEMAKE_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable SNAKEMAKE_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule simulations_create_training_or_test_distance_matrix (line 241, /tmp/tmp9156cwzx/simulations/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule simulations_grid_search_embed_training_or_test_data (line 274, /tmp/tmp9156cwzx/simulations/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule simulations_grid_search_accuracy (line 328, /tmp/tmp9156cwzx/simulations/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule simulations_aggregate_grid_search (line 378, /tmp/tmp9156cwzx/simulations/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule simulations_coronavirus_aggregate_grid_search_summaries (line 451, /tmp/tmp9156cwzx/simulations/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule simulations_influenza_aggregate_grid_search_summaries (line 485, /tmp/tmp9156cwzx/simulations/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule simulations_aggregate_all_grid_search_summaries (line 519, /tmp/tmp9156cwzx/simulations/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule simulations_representative_embed_pca (line 610, /tmp/tmp9156cwzx/simulations/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule simulations_representative_create_distance_matrix (line 657, /tmp/tmp9156cwzx/simulations/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule simulations_representative_embed_mds (line 690, /tmp/tmp9156cwzx/simulations/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule simulations_representative_embed_tsne (line 738, /tmp/tmp9156cwzx/simulations/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule simulations_representative_embed_umap (line 788, /tmp/tmp9156cwzx/simulations/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_deduplicate_sequences (line 39, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_parse (line 72, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_align (line 195, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_remove_reference_from_embedding_alignment (line 255, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_create_distance_matrix (line 289, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_embed_pca (line 322, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_embed_mds (line 379, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_embed_tsne (line 434, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_embed_umap (line 491, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_cluster (line 546, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_cluster_distances (line 596, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_get_table_of_tips (line 646, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_cluster_accuracy (line 675, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_concat_cluster_accuracy (line 725, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_plot_cluster_accuracy_by_parameter (line 767, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_get_optimal_cluster_parameters_and_accuracies (line 792, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_cluster_with_optimal_parameters (line 825, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_cluster_distances_with_optimal_parameters (line 876, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_calculate_internal_node_embedding_positions (line 926, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_create_node_output (line 962, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_create_node_output_for_genetic_clusters (line 995, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_tree (line 1028, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_ancestral (line 1184, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_translate (line 1240, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_clades (line 1283, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_create_table_from_tree_and_node_data (line 1325, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_export (line 1374, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_create_distance_dataframe (line 1426, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_infer_cluster_labels (line 1465, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_find_monophyletic_clusters (line 1508, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_annotate_embeddings (line 1557, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_scatterplot (line 1603, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_concat_mutation_tables (line 1792, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_concat_scatterplot_table (line 1836, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_within_between_stats (line 1885, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_concat_within_between_stats (line 1923, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_create_scatterplot_figure (line 1960, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_create_notebook_docs (line 1989, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_get_accessions (line 2023, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_get_authors_for_accessions (line 2058, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_clean (line 2096, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_deduplicate_sequences (line 38, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_parse (line 71, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_filter (line 114, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_align (line 175, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_remove_reference_from_embedding_alignment (line 219, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_tree (line 253, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_ancestral (line 393, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_translate (line 439, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_clades (line 482, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_create_distance_matrix (line 524, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_embed_pca (line 557, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_embed_mds (line 610, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_embed_tsne (line 661, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_embed_umap (line 714, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_cluster_with_optimal_parameters (line 765, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_cluster_distances_with_optimal_parameters (line 816, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_calculate_internal_node_embedding_positions (line 866, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_create_node_output (line 902, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_create_node_output_for_genetic_clusters (line 935, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_export (line 968, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_tree_to_table (line 1022, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_create_distance_dataframe (line 1075, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_infer_cluster_labels (line 1114, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_find_monophyletic_clusters (line 1157, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_annotate_embeddings (line 1206, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_get_table_of_tips (line 1252, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_cluster_accuracy (line 1281, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_concat_HDBSCAN_table (line 1331, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_concat_mutation_tables (line 1508, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_within_between_stats (line 1552, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_concat_within_between_stats (line 1590, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_scatterplot (line 1627, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_concat_scatterplot_table (line 1681, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_create_scatterplot_figure (line 1726, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_create_notebook_docs (line 1755, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_replication_subsample (line 1789, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_replication_align (line 1848, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_replication_remove_reference_from_alignment (line 1892, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_replication_create_distance_matrix (line 1926, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_replication_embed_pca (line 1959, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_replication_embed_mds (line 2001, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_replication_embed_tsne (line 2044, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_replication_embed_umap (line 2089, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_replication_cluster_with_optimal_parameters (line 2132, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_replication_cluster_distances_with_optimal_parameters (line 2180, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_replication_tree (line 2230, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_replication_root_and_prune_tree (line 2269, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_replication_refine (line 2312, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_replication_ancestral (line 2367, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_replication_translate (line 2410, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_replication_clades (line 2449, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_replication_tree_to_table (line 2487, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_replication_cluster_accuracy (line 2531, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_replication_aggregate_cluster_accuracy (line 2587, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_replication_plot_cluster_accuracy (line 2616, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_get_accessions (line 2641, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_get_authors_for_accessions (line 2676, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_split (line 57, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_deduplicate_sequences (line 91, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_parse (line 124, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_filter (line 167, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_pair_ha_strains (line 219, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_align (line 254, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_concat (line 298, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_tree (line 332, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_find_mccs (line 428, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_ancestral (line 571, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_translate (line 614, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_clades (line 653, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_create_distance_matrix (line 691, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_embed_pca (line 762, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_embed_mds (line 815, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_embed_tsne (line 866, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_embed_umap (line 919, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_cluster_with_optimal_parameters (line 970, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_cluster_distances_with_optimal_parameters (line 1021, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_create_node_output (line 1071, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_export (line 1104, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_create_table_from_tree_and_node_data (line 1159, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_create_distance_dataframe (line 1209, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_infer_cluster_labels (line 1260, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_find_monophyletic_clusters (line 1307, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_annotate_embeddings (line 1364, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_get_table_of_tips (line 1410, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_cluster_accuracy (line 1439, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_concat_HDBSCAN_table (line 1489, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_concat_mutation_tables (line 1596, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_within_between_stats (line 1640, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_concat_within_between_stats (line 1678, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_create_notebook_docs (line 1715, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_get_accessions (line 1763, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_get_authors_for_accessions (line 1798, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_aggregate_authors_for_accessions (line 1836, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_download_filtered_metadata (line 33, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_subsample_early_samples (line 62, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_download_all_aligned_sequences (line 116, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_extract_subsampled_data (line 145, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_uncompress_metadata (line 189, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_uncompress_alignment (line 269, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_embed_pca_before (line 298, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_bases_missing_vs_pc1 (line 352, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_tree (line 404, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_ancestral (line 518, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_translate (line 570, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_export (line 616, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_create_distance_matrix (line 667, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_embed_pca (line 740, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_embed_mds (line 793, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_embed_tsne (line 844, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_embed_umap (line 897, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_cluster (line 948, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_cluster_distances (line 998, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_cluster_accuracy (line 1048, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_concat_cluster_accuracy (line 1097, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_plot_cluster_accuracy_by_parameter (line 1139, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_get_optimal_cluster_parameters_and_accuracies (line 1164, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_cluster_with_optimal_parameters (line 1197, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_cluster_distances_with_optimal_parameters (line 1248, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_calculate_internal_node_embedding_positions (line 1298, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_create_node_output (line 1334, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_create_node_output_for_genetic_clusters (line 1367, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_tree_to_table (line 1400, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_create_distance_dataframe (line 1451, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_infer_cluster_labels (line 1487, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_find_monophyletic_clusters (line 1533, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_concat_monophyletic_clusters (line 1588, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_annotate_embeddings (line 1617, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_scatterplot (line 1663, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_concat_scatterplot_table (line 1721, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_create_scatterplot_figure (line 1766, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_get_table_of_tips (line 1858, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_concat_mutation_tables (line 1955, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_train_within_between_stats_clades (line 1999, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_train_within_between_stats_methods (line 2037, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_train_concat_within_between_stats_method (line 2075, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_train_concat_within_between_stats_clade_membership (line 2110, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_train_concat_within_between_stats (line 2145, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_create_notebook_docs (line 2206, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_get_accessions (line 2254, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_get_authors_for_accessions (line 2287, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_subsample_single_clade (line 2327, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_extract_subsampled_data_for_single_clade (line 2381, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_create_distance_matrix_for_single_clade (line 2476, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_embed_tsne_for_single_clade (line 2511, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_cluster_for_single_clade (line 2561, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_cluster_accuracy_for_single_clade (line 2609, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_cluster_accuracy_without_unclustered_for_single_clade (line 2658, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_select_lineages_for_single_clade (line 2707, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_select_clusters_for_single_clade (line 2736, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_merge_lineages_and_clusters_for_single_clade (line 2767, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_summarize_lineages_and_clusters_for_single_clade (line 2797, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_filter_lineages_and_clusters_for_single_clade (line 2826, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_plot_lineages_and_clusters_for_single_clade (line 2855, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_download_filtered_metadata (line 25, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_subsample_late_samples (line 54, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_download_official_pango_lineages (line 110, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_count_records_per_pango_lineage (line 138, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_get_distinct_well_covered_recombinant_lineages (line 171, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_filter_to_recombinant_metadata (line 217, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_subsample_late_recombinant_samples_and_parental_lineages (line 253, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_download_filtered_aligned_sequences (line 307, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_extract_subsampled_data (line 336, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_uncompress_metadata (line 381, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_uncompress_alignment (line 461, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_remove_reference_from_embedding_alignment (line 490, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_tree (line 524, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_ancestral (line 682, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_translate (line 734, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_export (line 780, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_create_distance_matrix (line 830, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_embed_pca (line 903, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_embed_mds (line 956, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_embed_tsne (line 1007, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_embed_umap (line 1060, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_cluster_with_optimal_parameters (line 1111, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_cluster_distances_with_optimal_parameters (line 1162, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_cluster_accuracy (line 1212, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_concat_cluster_accuracy (line 1261, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_create_node_output (line 1303, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_tree_to_table (line 1340, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_create_distance_dataframe (line 1391, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_infer_cluster_labels (line 1426, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_find_monophyletic_clusters (line 1472, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_concat_monophyletic_clusters (line 1527, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_annotate_embeddings (line 1556, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_scatterplot (line 1602, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_concat_scatterplot_table (line 1660, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_create_scatterplot_figure (line 1705, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_get_table_of_tips (line 1797, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_concat_mutation_tables (line 1894, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_get_distances_between_recombinant_and_parental_lineages (line 1938, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule sarscov2_test_concat_recombinant_distances (line 1988, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_within_between_stats_clades (line 2028, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_within_between_stats_methods (line 2066, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_concat_within_between_stats_method (line 2104, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_concat_within_between_stats_clade_membership (line 2139, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_concat_within_between_stats (line 2174, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_create_notebook_docs (line 2239, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_replication_subsample_metadata (line 2335, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_replication_subsample_sequences (line 2382, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_replication_create_distance_matrix (line 2412, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_replication_embed_pca (line 2485, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_replication_embed_mds (line 2527, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_replication_embed_tsne (line 2570, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_replication_embed_umap (line 2615, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_replication_cluster_with_optimal_parameters (line 2658, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_replication_cluster_distances_with_optimal_parameters (line 2706, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_replication_cluster_accuracy (line 2756, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_replication_aggregate_cluster_accuracy (line 2812, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_replication_plot_cluster_accuracy (line 2841, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_get_accessions (line 2867, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_get_authors_for_accessions (line 2900, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule within_between_stats (line 13, /tmp/tmp9156cwzx/manuscript/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule concat_mutation_tables (line 42, /tmp/tmp9156cwzx/manuscript/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule concat_monophyletic_clusters (line 83, /tmp/tmp9156cwzx/manuscript/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule concat_HDBSCAN_tables (line 124, /tmp/tmp9156cwzx/manuscript/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule concat_within_between_figure_table (line 200, /tmp/tmp9156cwzx/manuscript/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule concat_accessions_and_authors_tables (line 241, /tmp/tmp9156cwzx/manuscript/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule manuscript_plot_group_specific_mutations (line 276, /tmp/tmp9156cwzx/manuscript/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule manuscript_pdf (line 309, /tmp/tmp9156cwzx/manuscript/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule manuscript_html (line 360, /tmp/tmp9156cwzx/manuscript/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 4, - "subscribers_count": 7, - "topics": [], - "updated_at": 1724883197.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": "Knowledge Graph generator for WorkflowHub", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmph7kt2vg4/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "workflowhub-eu/workflowhub-graph", - "latest_release": null, - "linting": "Lints for rule source_ro_crates (line 12, /tmp/tmph7kt2vg4/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable OUTPUT_DIRS from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable VERSIONS from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable OUTPUT_DIRS from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable VERSIONS from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable OUTPUT_DIRS from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule report_created_files (line 35, /tmp/tmph7kt2vg4/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule merge_files (line 44, /tmp/tmph7kt2vg4/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n\nLints for rule create_ro_crate (line 70, /tmp/tmph7kt2vg4/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 4, - "subscribers_count": 9, - "topics": [], - "updated_at": 1726052509.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpd7wh6st6/greydongilmore-clinical_dicom2bids_smk-e56ae97/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpd7wh6st6/greydongilmore-clinical_dicom2bids_smk-e56ae97/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpd7wh6st6/greydongilmore-clinical_dicom2bids_smk-e56ae97/workflow/rules/fastsurfer.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpd7wh6st6/greydongilmore-clinical_dicom2bids_smk-e56ae97/workflow/rules/fmriprep.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpd7wh6st6/greydongilmore-clinical_dicom2bids_smk-e56ae97/workflow/rules/dicom2bids.smk\": Formatted content is different from original\n[INFO] 5 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "greydongilmore/clinical_dicom2bids_smk", - "latest_release": "stable", - "linting": "PermissionError in file /tmp/tmpd7wh6st6/greydongilmore-clinical_dicom2bids_smk-e56ae97/workflow/Snakefile, line 19:\n[Errno 13] Permission denied: \u0027/home/greydon\u0027\n File \"/tmp/tmpd7wh6st6/greydongilmore-clinical_dicom2bids_smk-e56ae97/workflow/Snakefile\", line 19, in \u003cmodule\u003e\n File \"\u003cfrozen os\u003e\", line 215, in makedirs\n File \"\u003cfrozen os\u003e\", line 215, in makedirs\n File \"\u003cfrozen os\u003e\", line 215, in makedirs\n File \"\u003cfrozen os\u003e\", line 215, in makedirs\n File \"\u003cfrozen os\u003e\", line 225, in makedirs\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 4, - "subscribers_count": 5, - "topics": [], - "updated_at": 1726284198.0 - }, - { - "config_readme": "\u003cp\u003eProvide experimental information in `config.yml``:\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003egenome: human # human or mouse\ngencode_genome_build: \"44\"\nfdr_cutoff: 0.05 # adj p value cut off for volcano plots\nfc_cutoff: 0.5 # log2 fold change cut off for volcano plots\nsalmon-quant: \n extra_params: \"\" # additional arguments to pass to Salmon\nsalmon-index:\n extra_params: \"--gencode\"\nresources: # computing resources\n trim:\n cpu: 8\n time: 60\n fastqc:\n cpu: 4\n time: 60\n mapping:\n cpu: 8\n time: 120\n deseq2:\n cpu: 6\n time: 60 \n plotting:\n cpu: 2\n time: 20\n\u003c/code\u003e\u003c/pre\u003e\n", - "data_format": 2, - "description": "Snakemake workflow for RNA-Seq differential transcript analysis using Salmon/Deseq2", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpb41cw1lx/niekwit-rna-seq-salmon-deseq2-b95b53c/workflow/rules/trimming.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpb41cw1lx/niekwit-rna-seq-salmon-deseq2-b95b53c/workflow/rules/deseq2.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpb41cw1lx/niekwit-rna-seq-salmon-deseq2-b95b53c/workflow/rules/mapping.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpb41cw1lx/niekwit-rna-seq-salmon-deseq2-b95b53c/workflow/rules/fastqc.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpb41cw1lx/niekwit-rna-seq-salmon-deseq2-b95b53c/workflow/rules/plotting.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpb41cw1lx/niekwit-rna-seq-salmon-deseq2-b95b53c/workflow/rules/resources.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpb41cw1lx/niekwit-rna-seq-salmon-deseq2-b95b53c/workflow/Snakefile\": Formatted content is different from original\n[INFO] 7 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "niekwit/rna-seq-salmon-deseq2", - "latest_release": "v0.7.0", - "linting": "Workflow version: v0.7.0\nWrapper version: v3.12.0\nValueError in file /tmp/tmpb41cw1lx/niekwit-rna-seq-salmon-deseq2-b95b53c/workflow/scripts/general_functions.smk, line 34:\nFollowing files not found:\nreads/WT_1_R1_001.fastq.gz\nreads/WT_1_R2_001.fastq.gz\nreads/WT_2_R1_001.fastq.gz\nreads/WT_2_R2_001.fastq.gz\nreads/WT_3_R1_001.fastq.gz\nreads/WT_3_R2_001.fastq.gz\nreads/KO_1_R1_001.fastq.gz\nreads/KO_1_R2_001.fastq.gz\nreads/KO_2_R1_001.fastq.gz\nreads/KO_2_R2_001.fastq.gz\nreads/KO_3_R1_001.fastq.gz\nreads/KO_3_R2_001.fastq.gz\n File \"/tmp/tmpb41cw1lx/niekwit-rna-seq-salmon-deseq2-b95b53c/workflow/Snakefile\", line 37, in \u003cmodule\u003e\n File \"/tmp/tmpb41cw1lx/niekwit-rna-seq-salmon-deseq2-b95b53c/workflow/scripts/general_functions.smk\", line 34, in samples\n", - "mandatory_flags": { - "desc": null, - "flags": null - }, - "report": true, - "software_stack_deployment": { - "conda": true, - "singularity": false, - "singularity+conda": false - }, - "standardized": true, - "stargazers_count": 4, - "subscribers_count": 1, - "topics": [ - "bioinformatics", - "snakemake", - "snakemake-workflow" - ], - "updated_at": 1726237495.0 - }, - { - "config_readme": "\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eConfiguration\u003c/h1\u003e\u003ca id=\"user-content-configuration\" class=\"anchor\" aria-label=\"Permalink: Configuration\" href=\"#configuration\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eUse the template \u003ccode\u003econfig.yaml\u003c/code\u003e to customize the workflow to your dataset. You\ncan find information about how the configuration works in the pipeline\u0027s\n\u003ca href=\"https://zjnolen.github.io/PopGLen\" rel=\"nofollow\"\u003edocumentation\u003c/a\u003e in the \"Configuration\"\nsection.\u003c/p\u003e\n", - "data_format": 2, - "description": "Bioinformatics pipeline to process whole genome resequencing data and perform genotype likelihood based population genomic analyses using ANGSD and related softwares. Flexible to datasets that combine high/low coverage and historical/fresh samples.", - "formatting": "[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmph92eamyp/zjnolen-PopGLen-52a27be/workflow/rules/0.2_ref_filt.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmph92eamyp/zjnolen-PopGLen-52a27be/workflow/rules/8.0_inbreeding.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] \n[INFO] 2 file(s) would be changed \ud83d\ude2c\n[INFO] 21 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", - "full_name": "zjnolen/PopGLen", - "latest_release": "v0.3.0", - "linting": null, - "mandatory_flags": null, - "report": true, - "software_stack_deployment": { - "singularity+conda": true - }, - "standardized": true, - "stargazers_count": 4, - "subscribers_count": 1, - "topics": [ - "snakemake", - "bioinformatics", - "bioinformatics-pipeline", - "genotype-likelihoods", - "population-genomics", - "whole-genome-sequencing", - "museomics", - "angsd" - ], - "updated_at": 1726668338.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": "Snakemake workflow for the preprocessing, alignment, QC, and quantification of spatial transcriptomics data", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpayc_xtqd/rules/0a_barcode_maps.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpayc_xtqd/Snakefile\": Keyword \"input\" at line 236 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpayc_xtqd/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[WARNING] In file \"/tmp/tmpayc_xtqd/rules/6a_scanpy_init.smk\": Keyword \"input\" at line 8 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmpayc_xtqd/rules/6a_scanpy_init.smk\": Keyword \"params\" at line 12 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmpayc_xtqd/rules/6a_scanpy_init.smk\": Keyword \"input\" at line 126 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[INFO] 2 file(s) would be changed \ud83d\ude2c\n[INFO] 2 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", - "full_name": "mckellardw/slide_snake", - "latest_release": null, - "linting": "Using workflow specific profile profiles/default for setting default command line arguments.\nLints for snakefile /tmp/tmpayc_xtqd/rules/0_utils.smk:\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n\nLints for snakefile /tmp/tmpayc_xtqd/rules/0a_barcode_maps.smk:\n * Path composition with \u0027+\u0027 in line 7:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n * Path composition with \u0027+\u0027 in line 78:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n\nLints for rule utils_index_BAM (line 5, /tmp/tmpayc_xtqd/rules/0_utils.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule BC_copy_barcode_map (line 5, /tmp/tmpayc_xtqd/rules/0a_barcode_maps.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n\nLints for rule BC_get_simple_whitelist (line 29, /tmp/tmpayc_xtqd/rules/0a_barcode_maps.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule BC_write_whitelist_variants (line 47, /tmp/tmpayc_xtqd/rules/0a_barcode_maps.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n\nLints for rule BC_insert_adapter_into_list (line 142, /tmp/tmpayc_xtqd/rules/0a_barcode_maps.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n\nLints for rule ilmn_1a_merge_fastqs (line 2, /tmp/tmpayc_xtqd/rules/short_read/1a_mergefqs.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n\nLints for rule ilmn_1b_R1_hardTrimming (line 136, /tmp/tmpayc_xtqd/rules/short_read/1b_trimming.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ilmn_1b_R1_internalTrimming (line 170, /tmp/tmpayc_xtqd/rules/short_read/1b_trimming.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ilmn_1c_fastQC_preTrim (line 5, /tmp/tmpayc_xtqd/rules/short_read/1c_fastqc.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule ilmn_1c_fastQC_postTrim (line 30, /tmp/tmpayc_xtqd/rules/short_read/1c_fastqc.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule ilmn_1c_fastQC_twiceTrim (line 54, /tmp/tmpayc_xtqd/rules/short_read/1c_fastqc.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule ilmn_2a_bwa_rRNA_filter_R1 (line 60, /tmp/tmpayc_xtqd/rules/short_read/2a_rRNA_bwa.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ilmn_2a_bwa_rRNA_compress_unmapped (line 82, /tmp/tmpayc_xtqd/rules/short_read/2a_rRNA_bwa.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ilmn_2a_bwa_rRNA_filtered_fastqc (line 99, /tmp/tmpayc_xtqd/rules/short_read/2a_rRNA_bwa.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule ilmn_2b_STAR_rRNA_align (line 7, /tmp/tmpayc_xtqd/rules/short_read/2b_rRNA_STAR.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n\nLints for rule ilmn_2b_STAR_rRNA_compress_outs (line 63, /tmp/tmpayc_xtqd/rules/short_read/2b_rRNA_STAR.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n * Param GENEDIR is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule ilmn_2b_STAR_rRNA_rename_compress_unmapped (line 99, /tmp/tmpayc_xtqd/rules/short_read/2b_rRNA_STAR.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n\nLints for rule ilmn_2b_STAR_rRNA_filtered_fastqc (line 122, /tmp/tmpayc_xtqd/rules/short_read/2b_rRNA_STAR.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule ilmn_2c_qualimapQC_rRNA_STAR (line 37, /tmp/tmpayc_xtqd/rules/short_read/2c_rRNA_qualimap.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule ilmn_2c_qualimap_summary2csv_rRNA_STAR (line 66, /tmp/tmpayc_xtqd/rules/short_read/2c_rRNA_qualimap.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ilmn_2d_ribodetector_get_noRibo_list (line 40, /tmp/tmpayc_xtqd/rules/short_read/2d_ribodetector.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ilmn_2d_ribodetector_gunzip_R1 (line 54, /tmp/tmpayc_xtqd/rules/short_read/2d_ribodetector.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ilmn_2d_ribodetector_filter_R1 (line 66, /tmp/tmpayc_xtqd/rules/short_read/2d_ribodetector.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ilmn_2d_ribodetector_filter_R1_internalTrim (line 82, /tmp/tmpayc_xtqd/rules/short_read/2d_ribodetector.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ilmn_2d_ribodetector_filter_R1_hardTrim (line 98, /tmp/tmpayc_xtqd/rules/short_read/2d_ribodetector.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ilmn_2d_ribodetector_compress_fqs (line 114, /tmp/tmpayc_xtqd/rules/short_read/2d_ribodetector.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ilmn_3a_STARsolo_align (line 9, /tmp/tmpayc_xtqd/rules/short_read/3a_star_align.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n\nLints for rule ilmn_3a_compress_STAR_outs (line 68, /tmp/tmpayc_xtqd/rules/short_read/3a_star_align.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n * Param VELDIR is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param GENEDIR is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param GENEFULLDIR is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule ilmn_3b_fastqc_unmapped (line 7, /tmp/tmpayc_xtqd/rules/short_read/3b_star_unmapped.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule ilmn_3c_strand_split_dedup_bam (line 30, /tmp/tmpayc_xtqd/rules/short_read/3c_star_dedup.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ilmn_3d_qualimapQC_STAR (line 3, /tmp/tmpayc_xtqd/rules/short_read/3d_star_qualimap.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule ilmn_3d_qualimap_summary2csv_STAR (line 31, /tmp/tmpayc_xtqd/rules/short_read/3d_star_qualimap.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ilmn_4a_kbpython_std_remove_suffix (line 65, /tmp/tmpayc_xtqd/rules/short_read/4a_kbpython.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule kbpython_std_compress_outs (line 81, /tmp/tmpayc_xtqd/rules/short_read/4a_kbpython.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ont_1a_merge_formats (line 5, /tmp/tmpayc_xtqd/rules/ont/1a_preprocessing.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ont_1a_readIDs_by_adapter_type (line 102, /tmp/tmpayc_xtqd/rules/ont/1a_preprocessing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ont_1a_adapter_scan_results (line 126, /tmp/tmpayc_xtqd/rules/ont/1a_preprocessing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ont_1a_merge_scan_lists (line 148, /tmp/tmpayc_xtqd/rules/ont/1a_preprocessing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ont_1a_subset_fastq_by_adapter_type (line 165, /tmp/tmpayc_xtqd/rules/ont/1a_preprocessing.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ont_1a_compress_merged_fq (line 194, /tmp/tmpayc_xtqd/rules/ont/1a_preprocessing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ont_1b_R1_hardTrimming (line 79, /tmp/tmpayc_xtqd/rules/ont/1b_trimming.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ont_1b_R1_internalTrim (line 109, /tmp/tmpayc_xtqd/rules/ont/1b_trimming.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ont_1c_fastq_call_bc_from_adapter (line 3, /tmp/tmpayc_xtqd/rules/ont/1c_barcode_calling.smk):\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n\nLints for rule ont_1c_filter_read_barcodes (line 64, /tmp/tmpayc_xtqd/rules/ont/1c_barcode_calling.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ont_1c_tsv_bc_correction (line 79, /tmp/tmpayc_xtqd/rules/ont/1c_barcode_calling.smk):\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n\nLints for rule ont_1d_sort_compress_output (line 45, /tmp/tmpayc_xtqd/rules/ont/1d_minimap2.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ont_1d_add_featureCounts_to_bam (line 137, /tmp/tmpayc_xtqd/rules/ont/1d_minimap2.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ont_1d_add_corrected_barcodes (line 166, /tmp/tmpayc_xtqd/rules/ont/1d_minimap2.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ont_1d_add_umis (line 194, /tmp/tmpayc_xtqd/rules/ont/1d_minimap2.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ont_1d_filter_bam_empty_tags (line 222, /tmp/tmpayc_xtqd/rules/ont/1d_minimap2.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ont_1d_counts_to_sparse (line 278, /tmp/tmpayc_xtqd/rules/ont/1d_minimap2.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule ont_clipBeforeSTAR (line 4, /tmp/tmpayc_xtqd/rules/ont/1d_STAR.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule ont_STARsolo_align (line 27, /tmp/tmpayc_xtqd/rules/ont/1d_STAR.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n\nLints for rule ont_compress_STAR_outs (line 119, /tmp/tmpayc_xtqd/rules/ont/1d_STAR.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n * Param VELDIR is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param GENEFULLDIR is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule ont_2_qualimap_minimap2 (line 2, /tmp/tmpayc_xtqd/rules/ont/2_qualimap.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule ont_2_qualimap_STAR (line 31, /tmp/tmpayc_xtqd/rules/ont/2_qualimap.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule ont_2_qualimap_summary2csv (line 60, /tmp/tmpayc_xtqd/rules/ont/2_qualimap.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ont_readQC_0_rawInput (line 2, /tmp/tmpayc_xtqd/rules/ont/2_read_qc.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ont_readQC_1_preCutadapt (line 26, /tmp/tmpayc_xtqd/rules/ont/2_read_qc.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ont_readQC_2_postCutadapt (line 50, /tmp/tmpayc_xtqd/rules/ont/2_read_qc.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ont_readQC_3_bam (line 89, /tmp/tmpayc_xtqd/rules/ont/2_read_qc.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule readQC_downsample (line 116, /tmp/tmpayc_xtqd/rules/ont/2_read_qc.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ont_readQC_summaryplot (line 133, /tmp/tmpayc_xtqd/rules/ont/2_read_qc.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule ont_fastQC_preTrim (line 2, /tmp/tmpayc_xtqd/rules/ont/2_fastqc.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule ont_fastQC_preCutadapt (line 25, /tmp/tmpayc_xtqd/rules/ont/2_fastqc.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule ont_fastQC_postCutadapt (line 48, /tmp/tmpayc_xtqd/rules/ont/2_fastqc.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 4, - "subscribers_count": 3, - "topics": [], - "updated_at": 1726929831.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": "Cut And Run Analysis Pipeline", - "formatting": "[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\s\u0027\n[DEBUG] In file \"/tmp/tmpr72wxess/CCBR-CARLISLE-0b1e117/workflow/rules/annotations.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpr72wxess/CCBR-CARLISLE-0b1e117/workflow/rules/align.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmpr72wxess/CCBR-CARLISLE-0b1e117/workflow/rules/init.smk\": NoParametersError: L354: In input definition.\n[DEBUG] In file \"/tmp/tmpr72wxess/CCBR-CARLISLE-0b1e117/workflow/rules/init.smk\": \n[DEBUG] In file \"/tmp/tmpr72wxess/CCBR-CARLISLE-0b1e117/workflow/rules/peakcalls.smk\": Formatted content is different from original\n[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\s\u0027\n[DEBUG] In file \"/tmp/tmpr72wxess/CCBR-CARLISLE-0b1e117/workflow/rules/qc.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpr72wxess/CCBR-CARLISLE-0b1e117/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpr72wxess/CCBR-CARLISLE-0b1e117/workflow/rules/diff.smk\": Formatted content is different from original\n[INFO] 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] 6 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "CCBR/CARLISLE", - "latest_release": "v2.6.0", - "linting": "IndexError in file /tmp/tmpr72wxess/CCBR-CARLISLE-0b1e117/workflow/rules/init.smk, line 43:\nlist index out of range\n File \"/tmp/tmpr72wxess/CCBR-CARLISLE-0b1e117/workflow/rules/init.smk\", line 43, in \u003cmodule\u003e\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 4, - "subscribers_count": 5, - "topics": [ - "pipeline", - "workflow" - ], - "updated_at": 1726843286.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpl34ftw0e/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "NeLLi-team/gvclass", - "latest_release": null, - "linting": "KeyError in file /tmp/tmpl34ftw0e/workflow/Snakefile, line 45:\n\u0027querydir\u0027\n File \"/tmp/tmpl34ftw0e/workflow/Snakefile\", line 45, in \u003cmodule\u003e\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 4, - "subscribers_count": 3, - "topics": [], - "updated_at": 1726785430.0 - }, - { - "config_readme": "\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eGeneral settings\u003c/h1\u003e\u003ca id=\"user-content-general-settings\" class=\"anchor\" aria-label=\"Permalink: General settings\" href=\"#general-settings\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eTo configure this workflow, modify \u003ccode\u003econfig/config.yaml\u003c/code\u003e according to your needs, following the explanations provided in the file.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eSample sheet\u003c/h1\u003e\u003ca id=\"user-content-sample-sheet\" class=\"anchor\" aria-label=\"Permalink: Sample sheet\" href=\"#sample-sheet\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eAdd samples to \u003ccode\u003econfig/samples.tsv\u003c/code\u003e. For each sample, the columns \u003ccode\u003esample_name\u003c/code\u003e, \u003ccode\u003ealias\u003c/code\u003e, \u003ccode\u003eplatform\u003c/code\u003e, and \u003ccode\u003egroup\u003c/code\u003e have to be defined.\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003eSamples within the same \u003ccode\u003egroup\u003c/code\u003e will be called jointly.\u003c/li\u003e\n\u003cli\u003eAliases represent the name of the sample within its group (they can be the same as the sample name, or something simpler, e.g. tumor or normal).\u003c/li\u003e\n\u003cli\u003eThe \u003ccode\u003eplatform\u003c/code\u003e column needs to contain the used sequencing plaform (one of \u0027CAPILLARY\u0027, \u0027LS454\u0027, \u0027ILLUMINA\u0027, \u0027SOLID\u0027, \u0027HELICOS\u0027, \u0027IONTORRENT\u0027, \u0027ONT\u0027, \u0027PACBIO\u2019).\u003c/li\u003e\n\u003cli\u003eThe \u003ccode\u003effpe\u003c/code\u003e column specifies whether a sample is a ffpe substrate (1) or not (0). ffpe treated normal samples are not supported.\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eMissing values can be specified by empty columns or by writing \u003ccode\u003eNA\u003c/code\u003e. Lines can be commented out with \u003ccode\u003e#\u003c/code\u003e.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eUnit sheet\u003c/h1\u003e\u003ca id=\"user-content-unit-sheet\" class=\"anchor\" aria-label=\"Permalink: Unit sheet\" href=\"#unit-sheet\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eFor each sample, add one or more sequencing units (runs, lanes or replicates) to the unit sheet \u003ccode\u003econfig/units.tsv\u003c/code\u003e.\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003eEach unit has a \u003ccode\u003eunit_name\u003c/code\u003e, which can be e.g. a running number, or an actual run, lane or replicate id.\u003c/li\u003e\n\u003cli\u003eEach unit has a \u003ccode\u003esample_name\u003c/code\u003e, which associates it with the biological sample it comes from.\u003c/li\u003e\n\u003cli\u003eFor each unit, define either one (column \u003ccode\u003efq1\u003c/code\u003e) or two (columns \u003ccode\u003efq1\u003c/code\u003e, \u003ccode\u003efq2\u003c/code\u003e) FASTQ files (these can point to anywhere in your system).\u003c/li\u003e\n\u003cli\u003eAlternatively, you can define an SRA (sequence read archive) accession (starting with e.g. ERR or SRR) by using a column \u003ccode\u003esra\u003c/code\u003e. In the latter case, the pipeline will automatically download the corresponding paired end reads from SRA. If both local files and SRA accession are available, the local files will be preferred.\u003c/li\u003e\n\u003cli\u003eDefine adapters in the \u003ccode\u003eadapters\u003c/code\u003e column, by putting \u003ca href=\"https://cutadapt.readthedocs.org\" rel=\"nofollow\"\u003ecutadapt arguments\u003c/a\u003e in quotation marks (e.g. \u003ccode\u003e\"-a ACGCGATCG -A GCTAGCGTACT\"\u003c/code\u003e).\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eMissing values can be specified by empty columns or by writing \u003ccode\u003eNA\u003c/code\u003e. Lines can be commented out with \u003ccode\u003e#\u003c/code\u003e.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003ePrimer trimming\u003c/h1\u003e\u003ca id=\"user-content-primer-trimming\" class=\"anchor\" aria-label=\"Permalink: Primer trimming\" href=\"#primer-trimming\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eFor panel data the pipeline allows trimming of amplicon primers on both ends of a fragment but also on a single end only.\nIn case of single end primers these are supposed to be located at the left end of a read.\nWhen primer trimming is enabled, primers have to be defined either directly in the \u003ccode\u003econfig.yaml\u003c/code\u003e or in a seperate tsv-file.\nDefining primers directly in the config file is prefered when all samples come from the same primer set.\nIn case of different panels, primers have to be set panel-wise in a seperate tsv-file (the path to that tsv can be set in the config under \u003ccode\u003eprimers/trimming/tsv\u003c/code\u003e).\nFor each panel the following columns need to be set: \u003ccode\u003epanel\u003c/code\u003e, \u003ccode\u003efa1\u003c/code\u003e and \u003ccode\u003efa2\u003c/code\u003e (optional).\nAdditionally, for each sample the corresponding panel must be defined in \u003ccode\u003esamples.tsv\u003c/code\u003e (column \u003ccode\u003epanel\u003c/code\u003e).\nFor single primer trimming only, the first entry in the config (respective in the tsv file) needs to be defined.\u003c/p\u003e\n", - "data_format": 2, - "description": "A flavor of https://github.com/snakemake-workflows/dna-seq-varlociraptor preconfigured for molecular tumor boards", - "formatting": null, - "full_name": "snakemake-workflows/dna-seq-mtb", - "latest_release": "v1.8.0", - "linting": null, - "mandatory_flags": null, - "report": true, - "software_stack_deployment": { - "conda": true, - "singularity": false, - "singularity+conda": false - }, - "standardized": true, - "stargazers_count": 4, - "subscribers_count": 2, - "topics": [], - "updated_at": 1721205075.0 - }, { "config_readme": null, "data_format": 2, @@ -49565,6 +49247,324 @@ var data = ], "updated_at": 1723580418.0 }, + { + "config_readme": null, + "data_format": 2, + "description": null, + "formatting": null, + "full_name": "Arcadia-Science/2024-Ecoli-amr-genotype-phenotype_7000strains", + "latest_release": "v1.0", + "linting": "Lints for rule create_file (line 6, /tmp/tmpc1lvu2e1/Arcadia-Science-2024-Ecoli-amr-genotype-phenotype_7000strains-21aa07e/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 4, + "subscribers_count": 2, + "topics": [], + "updated_at": 1726614952.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": null, + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp0odzv2xt/marschall-lab-strand-seq-graph-phasing-95e6472/workflow/rules/strandseq_breakpoints.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp0odzv2xt/marschall-lab-strand-seq-graph-phasing-95e6472/workflow/rules/sample_table.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp0odzv2xt/marschall-lab-strand-seq-graph-phasing-95e6472/workflow/rules/evaluate.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp0odzv2xt/marschall-lab-strand-seq-graph-phasing-95e6472/workflow/rules/collect_output.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp0odzv2xt/marschall-lab-strand-seq-graph-phasing-95e6472/workflow/rules/align_to_reference.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp0odzv2xt/marschall-lab-strand-seq-graph-phasing-95e6472/workflow/Snakefile\": Formatted content is different from original\n[INFO] 6 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "marschall-lab/strand-seq-graph-phasing", + "latest_release": "v0.5.01", + "linting": "KeyError in file /tmp/tmp0odzv2xt/marschall-lab-strand-seq-graph-phasing-95e6472/workflow/Snakefile, line 11:\n\u0027segmentLengthThreshold\u0027\n File \"/tmp/tmp0odzv2xt/marschall-lab-strand-seq-graph-phasing-95e6472/workflow/Snakefile\", line 11, in \u003cmodule\u003e\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 4, + "subscribers_count": 2, + "topics": [], + "updated_at": 1726760797.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": "MAGqual is a command line tool to evaluate the quality of metagenomic bins and generate recommended metadata in line with the MIMAG standards ", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpiawki_65/ac1513-MAGqual-14e7706/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "ac1513/MAGqual", + "latest_release": "v.0.3.0", + "linting": "Lints for snakefile /tmp/tmpiawki_65/ac1513-MAGqual-14e7706/workflow/Snakefile:\n * Path composition with \u0027+\u0027 in line 19:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n * Path composition with \u0027+\u0027 in line 1:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for rule bakta_db (line 51, /tmp/tmpiawki_65/ac1513-MAGqual-14e7706/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Shell command directly uses variable JOBID from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule bakta (line 109, /tmp/tmpiawki_65/ac1513-MAGqual-14e7706/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Param dir is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param database is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule checkm_db (line 160, /tmp/tmpiawki_65/ac1513-MAGqual-14e7706/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Shell command directly uses variable JOBID from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule checkm (line 216, /tmp/tmpiawki_65/ac1513-MAGqual-14e7706/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Shell command directly uses variable ext from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Param database is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule seqkit (line 272, /tmp/tmpiawki_65/ac1513-MAGqual-14e7706/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule high_mags (line 308, /tmp/tmpiawki_65/ac1513-MAGqual-14e7706/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Shell command directly uses variable ext from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Param out_loc is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule report_gen (line 361, /tmp/tmpiawki_65/ac1513-MAGqual-14e7706/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Shell command directly uses variable JOBID from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 4, + "subscribers_count": 1, + "topics": [ + "metagenomic-analysis", + "metagenomic-pipeline", + "metagenomics", + "snakemake", + "snakemake-pipeline" + ], + "updated_at": 1724849292.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": null, + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpa7c4q4jc/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "MetaSUB-CAMP/camp_short-read-quality-control", + "latest_release": null, + "linting": "Traceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1412, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpa7c4q4jc/workflow/Snakefile\", line 14, in \u003cmodule\u003e\n dirs = Workflow_Dirs(config[\u0027work_dir\u0027], \u0027short_read_qc\u0027)\n ^^^^^^^^^^^^^^^^^^^^^\n\nKeyError: \u0027work_dir\u0027\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 4, + "subscribers_count": 3, + "topics": [], + "updated_at": 1724523776.0 + }, + { + "config_readme": "\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eConfiguration\u003c/h2\u003e\u003ca id=\"user-content-configuration\" class=\"anchor\" aria-label=\"Permalink: Configuration\" href=\"#configuration\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003einput_dir\u003c/code\u003e : Path to the input folder, containing fastq files in compressed or decompressed format. The pipeline expects the input files to conform to 1 of 2 directory structures.\n1: \u003ccode\u003einput_dir\u003c/code\u003e contains subfolders for each sampleID/barcode, if that is the case all fastq files in each subfolder are concatenated and the subfolder name is used as a sample ID downstream. This is usually the \"fastq_pass\" folder from nanopore sequencing and basecalling output (atleast when using Guppy).\n2: \u003ccode\u003einput_dir\u003c/code\u003e contains already concatenated fastq files, directly located in \u003ccode\u003einput_dir\u003c/code\u003e. If that is the case, the pipeline uses the entire filename as a sample ID downstream. This is usually the case output from Dorado re-basecalling with demultiplexing enabled.\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003eoutput_dir\u003c/code\u003e: Output directory with the final results and a few intermediary files, that can be used for other downstream purposes if desired.\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003etmp_dir\u003c/code\u003e: Directory for temporary files.\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003elog_dir\u003c/code\u003e: Directory for log files for all invoked rules.\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003edb_path_sintax\u003c/code\u003e: Database to infer taxonomy using the SINTAX algorithm. Contains sequenceID, taxonomy string and fasta sequence.\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003edb_path_blast\u003c/code\u003e: Nucleotide blast formatted database to infer taxonomy using BLASTn algorithm.\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003eevalue\u003c/code\u003e: E-value cutoff for blast. Default = 1e-10.\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003elength_lower_limit\u003c/code\u003e: Argument passed on to \u003ccode\u003echopper\u003c/code\u003e for filtering reads. Appropriate values depends on amplicon length. This can be checked by running the helper script scripts/nanoplot.sh\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003elength_upper_limit\u003c/code\u003e: Argument passed on to \u003ccode\u003echopper\u003c/code\u003e for filtering reads. Appropriate values depends on amplicon length. This can be checked by running the helper script scripts/nanoplot.sh\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003equality_cut_off\u003c/code\u003e: Argument passed on to \u003ccode\u003echopper\u003c/code\u003e for filtering reads. Appropriate value depends on the quality of your sequencing data. This can be checked by running the helper script scripts/nanoplot.sh. It is recommended to pick a Q-score \u0026gt;20, if your data permits it.\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003emax_threads\u003c/code\u003e: Maximum number of threads that can be used for any rule.\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003einclude_blast_output\u003c/code\u003e: Default = True. If true snakemake will output a final OTU-table with taxonomy infered from a blastn search against a nt blast database.\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003einclude_sintax_output\u003c/code\u003e: Default = True. If true snakemake will output a final OTU-table with taxonomy infered from a sintax formatted database.\u003c/li\u003e\n\u003c/ul\u003e\n", + "data_format": 2, + "description": "Snakemake workflow to generate OTU tables from barcoded ONT data", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp3krq9hg_/MathiasEskildsen-ONT-AmpSeq-a883884/workflow/rules/09-fix_otu_table.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp3krq9hg_/MathiasEskildsen-ONT-AmpSeq-a883884/workflow/rules/13-ampvis2_std_plots.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp3krq9hg_/MathiasEskildsen-ONT-AmpSeq-a883884/workflow/rules/06-relabel.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp3krq9hg_/MathiasEskildsen-ONT-AmpSeq-a883884/workflow/rules/08-taxonomy.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp3krq9hg_/MathiasEskildsen-ONT-AmpSeq-a883884/workflow/rules/02-filtering.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp3krq9hg_/MathiasEskildsen-ONT-AmpSeq-a883884/workflow/rules/07-clustering_identity.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp3krq9hg_/MathiasEskildsen-ONT-AmpSeq-a883884/workflow/rules/04-mapping.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp3krq9hg_/MathiasEskildsen-ONT-AmpSeq-a883884/workflow/rules/capture_config.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp3krq9hg_/MathiasEskildsen-ONT-AmpSeq-a883884/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp3krq9hg_/MathiasEskildsen-ONT-AmpSeq-a883884/workflow/rules/12-phyloseq_abund_blast.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp3krq9hg_/MathiasEskildsen-ONT-AmpSeq-a883884/workflow/rules/10-prep_for_ampvis2.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp3krq9hg_/MathiasEskildsen-ONT-AmpSeq-a883884/workflow/rules/03-clustering.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp3krq9hg_/MathiasEskildsen-ONT-AmpSeq-a883884/workflow/rules/11-prep_for_phyloseq.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp3krq9hg_/MathiasEskildsen-ONT-AmpSeq-a883884/workflow/rules/01-concatenate_fastq.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp3krq9hg_/MathiasEskildsen-ONT-AmpSeq-a883884/workflow/rules/05-polish_racon.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp3krq9hg_/MathiasEskildsen-ONT-AmpSeq-a883884/workflow/Snakefile\": Formatted content is different from original\n[INFO] 16 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "MathiasEskildsen/ONT-AmpSeq", + "latest_release": "v1.1.1", + "linting": null, + "mandatory_flags": null, + "report": true, + "software_stack_deployment": { + "conda": true + }, + "standardized": true, + "stargazers_count": 4, + "subscribers_count": 1, + "topics": [], + "updated_at": 1725438827.0 + }, + { + "config_readme": "\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eCNVand Configuration Instructions\u003c/h1\u003e\u003ca id=\"user-content-cnvand-configuration-instructions\" class=\"anchor\" aria-label=\"Permalink: CNVand Configuration Instructions\" href=\"#cnvand-configuration-instructions\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eConfiguration File\u003c/h2\u003e\u003ca id=\"user-content-configuration-file\" class=\"anchor\" aria-label=\"Permalink: Configuration File\" href=\"#configuration-file\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThe configuration file (\u003ccode\u003econfig/config.yaml\u003c/code\u003e) contains various settings that the CNVand pipeline requires. Below is an example of a typical configuration file along with an explanation of each parameter.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003eExample Configuration File\u003c/h3\u003e\u003ca id=\"user-content-example-configuration-file\" class=\"anchor\" aria-label=\"Permalink: Example Configuration File\" href=\"#example-configuration-file\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cdiv class=\"highlight highlight-source-yaml\"\u003e\u003cpre\u003e\u003cspan class=\"pl-c\"\u003e\u003cspan class=\"pl-c\"\u003e#\u003c/span\u003e## Samplesheet\u003c/span\u003e\n\u003cspan class=\"pl-ent\"\u003esamples\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003econfig/samplesheet.tsv\u003c/span\u003e\n\n\u003cspan class=\"pl-c\"\u003e\u003cspan class=\"pl-c\"\u003e#\u003c/span\u003e## Output directory\u003c/span\u003e\n\u003cspan class=\"pl-ent\"\u003eoutdir\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003eoutput/\u003c/span\u003e\n\n\u003cspan class=\"pl-c\"\u003e\u003cspan class=\"pl-c\"\u003e#\u003c/span\u003e## Reference data\u003c/span\u003e\n\u003cspan class=\"pl-ent\"\u003eref\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003egenome\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003eworkflow/resources/Homo_sapiens_assembly38.fasta \u003c/span\u003e\u003cspan class=\"pl-c\"\u003e\u003cspan class=\"pl-c\"\u003e#\u003c/span\u003e Take care you\u0027re using the same reference in your full workflow\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003etarget_bed\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e.tests/integration/input/target.bed\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003eantitarget_bed\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e.tests/integration/input/antitarget.bed\u003c/span\u003e\n\n\u003cspan class=\"pl-c\"\u003e\u003cspan class=\"pl-c\"\u003e#\u003c/span\u003e## Toolkit parameter settings\u003c/span\u003e\n\u003cspan class=\"pl-ent\"\u003eparams\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003ecnvkit\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003etarget_coverage\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003eextra\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e-q 20\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003eantitarget_coverage\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003eextra\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e-q 20\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003ereference\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003eextra\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003ecall\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003eploidy\u003c/span\u003e: \u003cspan class=\"pl-c1\"\u003e2\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003eextra\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e \n \u003cspan class=\"pl-ent\"\u003ebintest\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003eextra\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e \n \u003cspan class=\"pl-ent\"\u003ebreaks\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003eextra\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e \n \u003cspan class=\"pl-ent\"\u003egenemetrics\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003eextra\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e \n \u003cspan class=\"pl-ent\"\u003escatter\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003ey_min\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e-2.5\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003eextra\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e \n \u003cspan class=\"pl-ent\"\u003eexport_vcf\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003eextra\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e \n \u003cspan class=\"pl-ent\"\u003esegment\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003eextra\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003eannotsv\u003c/span\u003e:\n \u003cspan class=\"pl-ent\"\u003eannotations\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003eworkflow/data/annotations/\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e \u003cspan class=\"pl-c\"\u003e\u003cspan class=\"pl-c\"\u003e#\u003c/span\u003e Annotations to be downloaded externally - see README.md for more details\u003c/span\u003e\n \u003cspan class=\"pl-ent\"\u003eextra\u003c/span\u003e: \u003cspan class=\"pl-s\"\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003cspan class=\"pl-pds\"\u003e\"\u003c/span\u003e\u003c/span\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003eParameter Explanations\u003c/h3\u003e\u003ca id=\"user-content-parameter-explanations\" class=\"anchor\" aria-label=\"Permalink: Parameter Explanations\" href=\"#parameter-explanations\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch4 class=\"heading-element\"\u003eSamplesheet\u003c/h4\u003e\u003ca id=\"user-content-samplesheet\" class=\"anchor\" aria-label=\"Permalink: Samplesheet\" href=\"#samplesheet\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003cstrong\u003esamples\u003c/strong\u003e: Path to the samplesheet file that contains information about the samples to be processed. This should be set to \u003ccode\u003econfig/samplesheet.tsv\u003c/code\u003e.\u003c/li\u003e\n\u003c/ul\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch4 class=\"heading-element\"\u003eOutput Directory\u003c/h4\u003e\u003ca id=\"user-content-output-directory\" class=\"anchor\" aria-label=\"Permalink: Output Directory\" href=\"#output-directory\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003cstrong\u003eoutdir\u003c/strong\u003e: Path to the directory where the output files will be stored. This is set to \u003ccode\u003eoutput/\u003c/code\u003e.\u003c/li\u003e\n\u003c/ul\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch4 class=\"heading-element\"\u003eReference Data\u003c/h4\u003e\u003ca id=\"user-content-reference-data\" class=\"anchor\" aria-label=\"Permalink: Reference Data\" href=\"#reference-data\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003cstrong\u003eref\u003c/strong\u003e:\n\u003cul\u003e\n\u003cli\u003e\n\u003cstrong\u003egenome\u003c/strong\u003e: Path to the reference genome file. Ensure that the reference genome used here is consistent throughout your workflow. Example: \u003ccode\u003eworkflow/resources/Homo_sapiens_assembly38.fasta\u003c/code\u003e.\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003etarget_bed\u003c/strong\u003e: Path to the target BED file. Example: \u003ccode\u003e.tests/integration/input/target.bed\u003c/code\u003e.\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003eantitarget_bed\u003c/strong\u003e: Path to the antitarget BED file. Example: \u003ccode\u003e.tests/integration/input/antitarget.bed\u003c/code\u003e.\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch4 class=\"heading-element\"\u003eToolkit Parameter Settings\u003c/h4\u003e\u003ca id=\"user-content-toolkit-parameter-settings\" class=\"anchor\" aria-label=\"Permalink: Toolkit Parameter Settings\" href=\"#toolkit-parameter-settings\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003cstrong\u003eparams\u003c/strong\u003e:\n\u003cul\u003e\n\u003cli\u003e\n\u003cstrong\u003ecnvkit\u003c/strong\u003e: Parameters for CNVkit tools.\n\u003cul\u003e\n\u003cli\u003e\n\u003cstrong\u003etarget_coverage\u003c/strong\u003e: Additional parameters for target coverage calculations. Example: \u003ccode\u003e-q 20\u003c/code\u003e.\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003eantitarget_coverage\u003c/strong\u003e: Additional parameters for antitarget coverage calculations. Example: \u003ccode\u003e-q 20\u003c/code\u003e.\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003ereference\u003c/strong\u003e: Additional parameters for reference generation.\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003ecall\u003c/strong\u003e: Parameters for CNV calling.\n\u003cul\u003e\n\u003cli\u003e\n\u003cstrong\u003eploidy\u003c/strong\u003e: Ploidy level to be used. Example: \u003ccode\u003e2\u003c/code\u003e.\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003eextra\u003c/strong\u003e: Additional parameters for the call step.\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003ebintest\u003c/strong\u003e: Additional parameters for bin testing.\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003ebreaks\u003c/strong\u003e: Additional parameters for breakpoints detection.\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003egenemetrics\u003c/strong\u003e: Additional parameters for gene metrics calculation.\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003escatter\u003c/strong\u003e: Parameters for scatter plot generation.\n\u003cul\u003e\n\u003cli\u003e\n\u003cstrong\u003ey_min\u003c/strong\u003e: Minimum y-axis value for scatter plots. Example: \u003ccode\u003e-2.5\u003c/code\u003e.\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003eextra\u003c/strong\u003e: Additional parameters for scatter plots.\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003eexport_vcf\u003c/strong\u003e: Additional parameters for VCF export.\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003esegment\u003c/strong\u003e: Additional parameters for segmentation.\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003eannotsv\u003c/strong\u003e: Parameters for AnnotSV tool.\n\u003cul\u003e\n\u003cli\u003e\n\u003cstrong\u003eannotations\u003c/strong\u003e: Path to the directory containing annotation files. Example: \u003ccode\u003eworkflow/data/annotations/\u003c/code\u003e.\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003eextra\u003c/strong\u003e: Additional parameters for AnnotSV.\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/li\u003e\n\u003c/ul\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eSamplesheet\u003c/h2\u003e\u003ca id=\"user-content-samplesheet-1\" class=\"anchor\" aria-label=\"Permalink: Samplesheet\" href=\"#samplesheet-1\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThe samplesheet (\u003ccode\u003econfig/samplesheet.tsv\u003c/code\u003e) contains information about the samples to be processed by the CNVand pipeline. It includes the sample name, path to the BAM file, and path to the VCF file.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003eExample Samplesheet\u003c/h3\u003e\u003ca id=\"user-content-example-samplesheet\" class=\"anchor\" aria-label=\"Permalink: Example Samplesheet\" href=\"#example-samplesheet\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cdiv class=\"highlight highlight-source-generic-db\"\u003e\u003cpre\u003e\u003cspan class=\"pl-c1\"\u003esample bam_path vcf_path\u003c/span\u003e\n\u003cspan class=\"pl-c1\"\u003eM24352 .tests/integration/input/M24352_CHR21.bam .tests/integration/input/M24352_CHR21.vcf.gz\u003c/span\u003e\u003c/pre\u003e\u003c/div\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003eColumn Explanations\u003c/h3\u003e\u003ca id=\"user-content-column-explanations\" class=\"anchor\" aria-label=\"Permalink: Column Explanations\" href=\"#column-explanations\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003cstrong\u003esample\u003c/strong\u003e: Unique identifier for the sample. Example: \u003ccode\u003eM24352\u003c/code\u003e.\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003ebam_path\u003c/strong\u003e: Path to the BAM file for the sample. Example: \u003ccode\u003e.tests/integration/input/M24352_CHR21.bam\u003c/code\u003e.\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003evcf_path\u003c/strong\u003e: Path to the VCF file for the sample. Example: \u003ccode\u003e.tests/integration/input/M24352_CHR21.vcf.gz\u003c/code\u003e.\u003c/li\u003e\n\u003c/ul\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eSummary\u003c/h2\u003e\u003ca id=\"user-content-summary\" class=\"anchor\" aria-label=\"Permalink: Summary\" href=\"#summary\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003col\u003e\n\u003cli\u003e\n\u003cstrong\u003eConfiguration File\u003c/strong\u003e: Ensure all paths and parameters are correctly set in the \u003ccode\u003econfig/config.yaml\u003c/code\u003e file.\u003c/li\u003e\n\u003cli\u003e\n\u003cstrong\u003eSamplesheet\u003c/strong\u003e: Ensure the \u003ccode\u003econfig/samplesheet.tsv\u003c/code\u003e file contains accurate paths to the BAM and VCF files for each sample.\u003c/li\u003e\n\u003c/ol\u003e\n\u003cp\u003eBy following these instructions, you will set up the CNVand pipeline correctly, ensuring accurate CNV analysis and annotation.\u003c/p\u003e\n", + "data_format": 2, + "description": "A snakemake workflow to analyse and annotate copy number variants", + "formatting": null, + "full_name": "IHGGM-Aachen/CNVand", + "latest_release": "0.3", + "linting": null, + "mandatory_flags": null, + "report": true, + "software_stack_deployment": { + "conda": true, + "singularity": false, + "singularity+conda": false + }, + "standardized": true, + "stargazers_count": 4, + "subscribers_count": 1, + "topics": [], + "updated_at": 1725145635.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": "A snakemake workflow based on the obitools suite of programs, that analyzes DNA metabarcoding data.", + "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmpap8ndjen/AnneSoBen-obitools_workflow-82f5ec5/workflow/Snakefile\": TabError: inconsistent use of tabs and spaces in indentation (\u003cstring\u003e, line 209)\n[INFO] In file \"/tmp/tmpap8ndjen/AnneSoBen-obitools_workflow-82f5ec5/workflow/Snakefile\": 1 file(s) raised parsing errors \ud83e\udd15\n\nsnakefmt version: 0.10.2", + "full_name": "AnneSoBen/obitools_workflow", + "latest_release": "v1.0.2", + "linting": "TabError in file \u003cstring\u003e, line 209:\ninconsistent use of tabs and spaces in indentation:\n\t\tuniq=folder_prefix+\"uniq\"\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/tokenize.py\", line 580, in _generate_tokens_from_c_tokenizer\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/tokenize.py\", line 576, in _generate_tokens_from_c_tokenizer\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 4, + "subscribers_count": 2, + "topics": [ + "edna", + "metabarcoding", + "bioinformatics-pipeline", + "edna-pipeline" + ], + "updated_at": 1725781796.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": "Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2", + "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmp9156cwzx/Snakefile\": Keyword \"input\" at line 98 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmp9156cwzx/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "blab/cartography", + "latest_release": null, + "linting": "/tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile:808: SyntaxWarning: invalid escape sequence \u0027\\-\u0027\n rule seasonal_flu_training_concat_scatterplot_table:\n/tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile:818: SyntaxWarning: invalid escape sequence \u0027\\-\u0027\n column = \"pearson_coef\",\n/tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile:1180: SyntaxWarning: invalid escape sequence \u0027\\-\u0027\n \n/tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile:1190: SyntaxWarning: invalid escape sequence \u0027\\-\u0027\n shell:\n/tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile:2752: SyntaxWarning: invalid escape sequence \u0027\\-\u0027\n/tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile:2761: SyntaxWarning: invalid escape sequence \u0027\\-\u0027\n/tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile:2813: SyntaxWarning: invalid escape sequence \u0027\\-\u0027\n/tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile:2821: SyntaxWarning: invalid escape sequence \u0027\\-\u0027\n/tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile:2842: SyntaxWarning: invalid escape sequence \u0027\\-\u0027\n/tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile:2850: SyntaxWarning: invalid escape sequence \u0027\\-\u0027\nLints for snakefile /tmp/tmp9156cwzx/simulations/Snakefile:\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n\nLints for snakefile /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile:\n * Path composition with \u0027+\u0027 in line 899:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile:\n * Path composition with \u0027+\u0027 in line 1160:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile:\n * Path composition with \u0027+\u0027 in line 808:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n Also see:\n\n\nLints for snakefile /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile:\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n\nLints for snakefile /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile:\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n\nLints for rule simulations_run_simulation (line 36, /tmp/tmp9156cwzx/simulations/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Shell command directly uses variable SNAKEMAKE_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable SNAKEMAKE_DIR from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule simulations_create_training_or_test_distance_matrix (line 241, /tmp/tmp9156cwzx/simulations/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule simulations_grid_search_embed_training_or_test_data (line 274, /tmp/tmp9156cwzx/simulations/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule simulations_grid_search_accuracy (line 328, /tmp/tmp9156cwzx/simulations/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule simulations_aggregate_grid_search (line 378, /tmp/tmp9156cwzx/simulations/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule simulations_coronavirus_aggregate_grid_search_summaries (line 451, /tmp/tmp9156cwzx/simulations/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule simulations_influenza_aggregate_grid_search_summaries (line 485, /tmp/tmp9156cwzx/simulations/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule simulations_aggregate_all_grid_search_summaries (line 519, /tmp/tmp9156cwzx/simulations/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule simulations_representative_embed_pca (line 610, /tmp/tmp9156cwzx/simulations/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule simulations_representative_create_distance_matrix (line 657, /tmp/tmp9156cwzx/simulations/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule simulations_representative_embed_mds (line 690, /tmp/tmp9156cwzx/simulations/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule simulations_representative_embed_tsne (line 738, /tmp/tmp9156cwzx/simulations/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule simulations_representative_embed_umap (line 788, /tmp/tmp9156cwzx/simulations/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_deduplicate_sequences (line 39, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_parse (line 72, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_align (line 195, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_remove_reference_from_embedding_alignment (line 255, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_create_distance_matrix (line 289, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_embed_pca (line 322, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_embed_mds (line 379, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_embed_tsne (line 434, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_embed_umap (line 491, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_cluster (line 546, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_cluster_distances (line 596, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_get_table_of_tips (line 646, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_cluster_accuracy (line 675, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_concat_cluster_accuracy (line 725, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_plot_cluster_accuracy_by_parameter (line 767, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_get_optimal_cluster_parameters_and_accuracies (line 792, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_cluster_with_optimal_parameters (line 825, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_cluster_distances_with_optimal_parameters (line 876, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_calculate_internal_node_embedding_positions (line 926, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_create_node_output (line 962, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_create_node_output_for_genetic_clusters (line 995, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_tree (line 1028, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_ancestral (line 1184, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_translate (line 1240, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_clades (line 1283, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_create_table_from_tree_and_node_data (line 1325, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_export (line 1374, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_create_distance_dataframe (line 1426, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_infer_cluster_labels (line 1465, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_find_monophyletic_clusters (line 1508, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_annotate_embeddings (line 1557, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_scatterplot (line 1603, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_concat_mutation_tables (line 1792, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_concat_scatterplot_table (line 1836, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_within_between_stats (line 1885, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_concat_within_between_stats (line 1923, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_create_scatterplot_figure (line 1960, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_create_notebook_docs (line 1989, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_get_accessions (line 2023, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_get_authors_for_accessions (line 2058, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_training_clean (line 2096, /tmp/tmp9156cwzx/seasonal-flu-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_deduplicate_sequences (line 38, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_parse (line 71, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_filter (line 114, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_align (line 175, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_remove_reference_from_embedding_alignment (line 219, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_tree (line 253, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_ancestral (line 393, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_translate (line 439, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_clades (line 482, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_create_distance_matrix (line 524, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_embed_pca (line 557, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_embed_mds (line 610, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_embed_tsne (line 661, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_embed_umap (line 714, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_cluster_with_optimal_parameters (line 765, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_cluster_distances_with_optimal_parameters (line 816, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_calculate_internal_node_embedding_positions (line 866, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_create_node_output (line 902, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_create_node_output_for_genetic_clusters (line 935, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_export (line 968, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_tree_to_table (line 1022, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_create_distance_dataframe (line 1075, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_infer_cluster_labels (line 1114, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_find_monophyletic_clusters (line 1157, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_annotate_embeddings (line 1206, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_get_table_of_tips (line 1252, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_cluster_accuracy (line 1281, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_concat_HDBSCAN_table (line 1331, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_concat_mutation_tables (line 1508, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_within_between_stats (line 1552, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_concat_within_between_stats (line 1590, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_scatterplot (line 1627, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_concat_scatterplot_table (line 1681, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_create_scatterplot_figure (line 1726, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_create_notebook_docs (line 1755, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_replication_subsample (line 1789, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_replication_align (line 1848, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_replication_remove_reference_from_alignment (line 1892, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_replication_create_distance_matrix (line 1926, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_replication_embed_pca (line 1959, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_replication_embed_mds (line 2001, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_replication_embed_tsne (line 2044, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_replication_embed_umap (line 2089, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_replication_cluster_with_optimal_parameters (line 2132, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_replication_cluster_distances_with_optimal_parameters (line 2180, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_replication_tree (line 2230, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_replication_root_and_prune_tree (line 2269, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_replication_refine (line 2312, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_replication_ancestral (line 2367, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_replication_translate (line 2410, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_replication_clades (line 2449, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_replication_tree_to_table (line 2487, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_replication_cluster_accuracy (line 2531, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_replication_aggregate_cluster_accuracy (line 2587, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_replication_plot_cluster_accuracy (line 2616, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_get_accessions (line 2641, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_test_get_authors_for_accessions (line 2676, /tmp/tmp9156cwzx/seasonal-flu-nextstrain-2018-2020/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_split (line 57, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_deduplicate_sequences (line 91, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_parse (line 124, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_filter (line 167, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_pair_ha_strains (line 219, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_align (line 254, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_concat (line 298, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_tree (line 332, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_find_mccs (line 428, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_ancestral (line 571, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_translate (line 614, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_clades (line 653, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_create_distance_matrix (line 691, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_embed_pca (line 762, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_embed_mds (line 815, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_embed_tsne (line 866, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_embed_umap (line 919, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_cluster_with_optimal_parameters (line 970, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_cluster_distances_with_optimal_parameters (line 1021, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_create_node_output (line 1071, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_export (line 1104, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_create_table_from_tree_and_node_data (line 1159, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_create_distance_dataframe (line 1209, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_infer_cluster_labels (line 1260, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_find_monophyletic_clusters (line 1307, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_annotate_embeddings (line 1364, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_get_table_of_tips (line 1410, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_cluster_accuracy (line 1439, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_concat_HDBSCAN_table (line 1489, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_concat_mutation_tables (line 1596, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_within_between_stats (line 1640, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_concat_within_between_stats (line 1678, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_create_notebook_docs (line 1715, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_get_accessions (line 1763, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_get_authors_for_accessions (line 1798, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule seasonal_flu_reassortment_aggregate_authors_for_accessions (line 1836, /tmp/tmp9156cwzx/ha-na-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_download_filtered_metadata (line 33, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_subsample_early_samples (line 62, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_download_all_aligned_sequences (line 116, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_extract_subsampled_data (line 145, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_uncompress_metadata (line 189, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_uncompress_alignment (line 269, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_embed_pca_before (line 298, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_bases_missing_vs_pc1 (line 352, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_tree (line 404, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_ancestral (line 518, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_translate (line 570, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_export (line 616, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_create_distance_matrix (line 667, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_embed_pca (line 740, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_embed_mds (line 793, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_embed_tsne (line 844, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_embed_umap (line 897, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_cluster (line 948, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_cluster_distances (line 998, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_cluster_accuracy (line 1048, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_concat_cluster_accuracy (line 1097, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_plot_cluster_accuracy_by_parameter (line 1139, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_get_optimal_cluster_parameters_and_accuracies (line 1164, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_cluster_with_optimal_parameters (line 1197, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_cluster_distances_with_optimal_parameters (line 1248, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_calculate_internal_node_embedding_positions (line 1298, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_create_node_output (line 1334, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_create_node_output_for_genetic_clusters (line 1367, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_tree_to_table (line 1400, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_create_distance_dataframe (line 1451, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_infer_cluster_labels (line 1487, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_find_monophyletic_clusters (line 1533, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_concat_monophyletic_clusters (line 1588, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_annotate_embeddings (line 1617, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_scatterplot (line 1663, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_concat_scatterplot_table (line 1721, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_create_scatterplot_figure (line 1766, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_get_table_of_tips (line 1858, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_concat_mutation_tables (line 1955, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_train_within_between_stats_clades (line 1999, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_train_within_between_stats_methods (line 2037, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_train_concat_within_between_stats_method (line 2075, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_train_concat_within_between_stats_clade_membership (line 2110, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_train_concat_within_between_stats (line 2145, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_create_notebook_docs (line 2206, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_get_accessions (line 2254, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_get_authors_for_accessions (line 2287, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_subsample_single_clade (line 2327, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_extract_subsampled_data_for_single_clade (line 2381, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_create_distance_matrix_for_single_clade (line 2476, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_embed_tsne_for_single_clade (line 2511, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_cluster_for_single_clade (line 2561, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_cluster_accuracy_for_single_clade (line 2609, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_cluster_accuracy_without_unclustered_for_single_clade (line 2658, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_select_lineages_for_single_clade (line 2707, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_select_clusters_for_single_clade (line 2736, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_merge_lineages_and_clusters_for_single_clade (line 2767, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_summarize_lineages_and_clusters_for_single_clade (line 2797, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_filter_lineages_and_clusters_for_single_clade (line 2826, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_plot_lineages_and_clusters_for_single_clade (line 2855, /tmp/tmp9156cwzx/sars-cov-2-nextstrain/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_download_filtered_metadata (line 25, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_subsample_late_samples (line 54, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_download_official_pango_lineages (line 110, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_count_records_per_pango_lineage (line 138, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_get_distinct_well_covered_recombinant_lineages (line 171, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_filter_to_recombinant_metadata (line 217, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_subsample_late_recombinant_samples_and_parental_lineages (line 253, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_download_filtered_aligned_sequences (line 307, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_extract_subsampled_data (line 336, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_uncompress_metadata (line 381, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_uncompress_alignment (line 461, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_remove_reference_from_embedding_alignment (line 490, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_tree (line 524, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_ancestral (line 682, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_translate (line 734, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_export (line 780, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_create_distance_matrix (line 830, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_embed_pca (line 903, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_embed_mds (line 956, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_embed_tsne (line 1007, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_embed_umap (line 1060, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_cluster_with_optimal_parameters (line 1111, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_cluster_distances_with_optimal_parameters (line 1162, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_cluster_accuracy (line 1212, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_concat_cluster_accuracy (line 1261, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_create_node_output (line 1303, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_tree_to_table (line 1340, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_create_distance_dataframe (line 1391, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_infer_cluster_labels (line 1426, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_find_monophyletic_clusters (line 1472, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_concat_monophyletic_clusters (line 1527, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_annotate_embeddings (line 1556, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_scatterplot (line 1602, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_concat_scatterplot_table (line 1660, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_create_scatterplot_figure (line 1705, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_get_table_of_tips (line 1797, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_concat_mutation_tables (line 1894, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_get_distances_between_recombinant_and_parental_lineages (line 1938, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule sarscov2_test_concat_recombinant_distances (line 1988, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_within_between_stats_clades (line 2028, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_within_between_stats_methods (line 2066, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_concat_within_between_stats_method (line 2104, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_concat_within_between_stats_clade_membership (line 2139, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_concat_within_between_stats (line 2174, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_create_notebook_docs (line 2239, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_replication_subsample_metadata (line 2335, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_replication_subsample_sequences (line 2382, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_replication_create_distance_matrix (line 2412, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_replication_embed_pca (line 2485, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_replication_embed_mds (line 2527, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_replication_embed_tsne (line 2570, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_replication_embed_umap (line 2615, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_replication_cluster_with_optimal_parameters (line 2658, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_replication_cluster_distances_with_optimal_parameters (line 2706, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_replication_cluster_accuracy (line 2756, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_replication_aggregate_cluster_accuracy (line 2812, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_replication_plot_cluster_accuracy (line 2841, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_get_accessions (line 2867, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule sarscov2_test_get_authors_for_accessions (line 2900, /tmp/tmp9156cwzx/sars-cov-2-nextstrain-2022-2023/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule within_between_stats (line 13, /tmp/tmp9156cwzx/manuscript/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule concat_mutation_tables (line 42, /tmp/tmp9156cwzx/manuscript/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule concat_monophyletic_clusters (line 83, /tmp/tmp9156cwzx/manuscript/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule concat_HDBSCAN_tables (line 124, /tmp/tmp9156cwzx/manuscript/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule concat_within_between_figure_table (line 200, /tmp/tmp9156cwzx/manuscript/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule concat_accessions_and_authors_tables (line 241, /tmp/tmp9156cwzx/manuscript/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule manuscript_plot_group_specific_mutations (line 276, /tmp/tmp9156cwzx/manuscript/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule manuscript_pdf (line 309, /tmp/tmp9156cwzx/manuscript/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule manuscript_html (line 360, /tmp/tmp9156cwzx/manuscript/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 4, + "subscribers_count": 7, + "topics": [], + "updated_at": 1724883197.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": "Knowledge Graph generator for WorkflowHub", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmph7kt2vg4/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "workflowhub-eu/workflowhub-graph", + "latest_release": null, + "linting": "Lints for rule source_ro_crates (line 12, /tmp/tmph7kt2vg4/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n * Shell command directly uses variable OUTPUT_DIRS from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable VERSIONS from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable OUTPUT_DIRS from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable VERSIONS from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n * Shell command directly uses variable OUTPUT_DIRS from outside of the rule:\n It is recommended to pass all files as input and output, and non-file\n parameters via the params directive. Otherwise, provenance tracking is\n less accurate.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n\nLints for rule report_created_files (line 35, /tmp/tmph7kt2vg4/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule merge_files (line 44, /tmp/tmph7kt2vg4/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n\nLints for rule create_ro_crate (line 70, /tmp/tmph7kt2vg4/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 4, + "subscribers_count": 9, + "topics": [], + "updated_at": 1726052509.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": null, + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpd7wh6st6/greydongilmore-clinical_dicom2bids_smk-e56ae97/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpd7wh6st6/greydongilmore-clinical_dicom2bids_smk-e56ae97/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpd7wh6st6/greydongilmore-clinical_dicom2bids_smk-e56ae97/workflow/rules/fastsurfer.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpd7wh6st6/greydongilmore-clinical_dicom2bids_smk-e56ae97/workflow/rules/fmriprep.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpd7wh6st6/greydongilmore-clinical_dicom2bids_smk-e56ae97/workflow/rules/dicom2bids.smk\": Formatted content is different from original\n[INFO] 5 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "greydongilmore/clinical_dicom2bids_smk", + "latest_release": "stable", + "linting": "PermissionError in file /tmp/tmpd7wh6st6/greydongilmore-clinical_dicom2bids_smk-e56ae97/workflow/Snakefile, line 19:\n[Errno 13] Permission denied: \u0027/home/greydon\u0027\n File \"/tmp/tmpd7wh6st6/greydongilmore-clinical_dicom2bids_smk-e56ae97/workflow/Snakefile\", line 19, in \u003cmodule\u003e\n File \"\u003cfrozen os\u003e\", line 215, in makedirs\n File \"\u003cfrozen os\u003e\", line 215, in makedirs\n File \"\u003cfrozen os\u003e\", line 215, in makedirs\n File \"\u003cfrozen os\u003e\", line 215, in makedirs\n File \"\u003cfrozen os\u003e\", line 225, in makedirs\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 4, + "subscribers_count": 5, + "topics": [], + "updated_at": 1726284198.0 + }, + { + "config_readme": "\u003cp\u003eProvide experimental information in `config.yml``:\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003egenome: human # human or mouse\ngencode_genome_build: \"44\"\nfdr_cutoff: 0.05 # adj p value cut off for volcano plots\nfc_cutoff: 0.5 # log2 fold change cut off for volcano plots\nsalmon-quant: \n extra_params: \"\" # additional arguments to pass to Salmon\nsalmon-index:\n extra_params: \"--gencode\"\nresources: # computing resources\n trim:\n cpu: 8\n time: 60\n fastqc:\n cpu: 4\n time: 60\n mapping:\n cpu: 8\n time: 120\n deseq2:\n cpu: 6\n time: 60 \n plotting:\n cpu: 2\n time: 20\n\u003c/code\u003e\u003c/pre\u003e\n", + "data_format": 2, + "description": "Snakemake workflow for RNA-Seq differential transcript analysis using Salmon/Deseq2", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpb41cw1lx/niekwit-rna-seq-salmon-deseq2-b95b53c/workflow/rules/trimming.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpb41cw1lx/niekwit-rna-seq-salmon-deseq2-b95b53c/workflow/rules/deseq2.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpb41cw1lx/niekwit-rna-seq-salmon-deseq2-b95b53c/workflow/rules/mapping.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpb41cw1lx/niekwit-rna-seq-salmon-deseq2-b95b53c/workflow/rules/fastqc.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpb41cw1lx/niekwit-rna-seq-salmon-deseq2-b95b53c/workflow/rules/plotting.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpb41cw1lx/niekwit-rna-seq-salmon-deseq2-b95b53c/workflow/rules/resources.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpb41cw1lx/niekwit-rna-seq-salmon-deseq2-b95b53c/workflow/Snakefile\": Formatted content is different from original\n[INFO] 7 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "niekwit/rna-seq-salmon-deseq2", + "latest_release": "v0.7.0", + "linting": "Workflow version: v0.7.0\nWrapper version: v3.12.0\nValueError in file /tmp/tmpb41cw1lx/niekwit-rna-seq-salmon-deseq2-b95b53c/workflow/scripts/general_functions.smk, line 34:\nFollowing files not found:\nreads/WT_1_R1_001.fastq.gz\nreads/WT_1_R2_001.fastq.gz\nreads/WT_2_R1_001.fastq.gz\nreads/WT_2_R2_001.fastq.gz\nreads/WT_3_R1_001.fastq.gz\nreads/WT_3_R2_001.fastq.gz\nreads/KO_1_R1_001.fastq.gz\nreads/KO_1_R2_001.fastq.gz\nreads/KO_2_R1_001.fastq.gz\nreads/KO_2_R2_001.fastq.gz\nreads/KO_3_R1_001.fastq.gz\nreads/KO_3_R2_001.fastq.gz\n File \"/tmp/tmpb41cw1lx/niekwit-rna-seq-salmon-deseq2-b95b53c/workflow/Snakefile\", line 37, in \u003cmodule\u003e\n File \"/tmp/tmpb41cw1lx/niekwit-rna-seq-salmon-deseq2-b95b53c/workflow/scripts/general_functions.smk\", line 34, in samples\n", + "mandatory_flags": { + "desc": null, + "flags": null + }, + "report": true, + "software_stack_deployment": { + "conda": true, + "singularity": false, + "singularity+conda": false + }, + "standardized": true, + "stargazers_count": 4, + "subscribers_count": 1, + "topics": [ + "bioinformatics", + "snakemake", + "snakemake-workflow" + ], + "updated_at": 1726237495.0 + }, + { + "config_readme": "\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eConfiguration\u003c/h1\u003e\u003ca id=\"user-content-configuration\" class=\"anchor\" aria-label=\"Permalink: Configuration\" href=\"#configuration\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eUse the template \u003ccode\u003econfig.yaml\u003c/code\u003e to customize the workflow to your dataset. You\ncan find information about how the configuration works in the pipeline\u0027s\n\u003ca href=\"https://zjnolen.github.io/PopGLen\" rel=\"nofollow\"\u003edocumentation\u003c/a\u003e in the \"Configuration\"\nsection.\u003c/p\u003e\n", + "data_format": 2, + "description": "Bioinformatics pipeline to process whole genome resequencing data and perform genotype likelihood based population genomic analyses using ANGSD and related softwares. Flexible to datasets that combine high/low coverage and historical/fresh samples.", + "formatting": "[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmph92eamyp/zjnolen-PopGLen-52a27be/workflow/rules/0.2_ref_filt.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] \n[DEBUG] In file \"/tmp/tmph92eamyp/zjnolen-PopGLen-52a27be/workflow/rules/8.0_inbreeding.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[DEBUG] \n[INFO] 2 file(s) would be changed \ud83d\ude2c\n[INFO] 21 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", + "full_name": "zjnolen/PopGLen", + "latest_release": "v0.3.0", + "linting": null, + "mandatory_flags": null, + "report": true, + "software_stack_deployment": { + "singularity+conda": true + }, + "standardized": true, + "stargazers_count": 4, + "subscribers_count": 1, + "topics": [ + "snakemake", + "bioinformatics", + "bioinformatics-pipeline", + "genotype-likelihoods", + "population-genomics", + "whole-genome-sequencing", + "museomics", + "angsd" + ], + "updated_at": 1726668338.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": "Snakemake workflow for the preprocessing, alignment, QC, and quantification of spatial transcriptomics data", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpayc_xtqd/rules/0a_barcode_maps.smk\": Formatted content is different from original\n[DEBUG] \n[WARNING] In file \"/tmp/tmpayc_xtqd/Snakefile\": Keyword \"input\" at line 236 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpayc_xtqd/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] \n[WARNING] In file \"/tmp/tmpayc_xtqd/rules/6a_scanpy_init.smk\": Keyword \"input\" at line 8 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmpayc_xtqd/rules/6a_scanpy_init.smk\": Keyword \"params\" at line 12 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[WARNING] In file \"/tmp/tmpayc_xtqd/rules/6a_scanpy_init.smk\": Keyword \"input\" at line 126 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[INFO] 2 file(s) would be changed \ud83d\ude2c\n[INFO] 2 file(s) would be left unchanged \ud83c\udf89\n\nsnakefmt version: 0.10.2", + "full_name": "mckellardw/slide_snake", + "latest_release": null, + "linting": "Using workflow specific profile profiles/default for setting default command line arguments.\nLints for snakefile /tmp/tmpayc_xtqd/rules/0_utils.smk:\n * Mixed rules and functions in same snakefile.:\n Small one-liner functions used only once should be defined as lambda\n expressions. Other functions should be collected in a common module, e.g.\n \u0027rules/common.smk\u0027. This makes the workflow steps more readable.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes\n\nLints for snakefile /tmp/tmpayc_xtqd/rules/0a_barcode_maps.smk:\n * Path composition with \u0027+\u0027 in line 7:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n * Path composition with \u0027+\u0027 in line 78:\n This becomes quickly unreadable. Usually, it is better to endure some\n redundancy against having a more readable workflow. Hence, just repeat\n common prefixes. If path composition is unavoidable, use pathlib or\n (python \u003e= 3.6) string formatting with f\"...\".\n\nLints for rule utils_index_BAM (line 5, /tmp/tmpayc_xtqd/rules/0_utils.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule BC_copy_barcode_map (line 5, /tmp/tmpayc_xtqd/rules/0a_barcode_maps.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n\nLints for rule BC_get_simple_whitelist (line 29, /tmp/tmpayc_xtqd/rules/0a_barcode_maps.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule BC_write_whitelist_variants (line 47, /tmp/tmpayc_xtqd/rules/0a_barcode_maps.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n\nLints for rule BC_insert_adapter_into_list (line 142, /tmp/tmpayc_xtqd/rules/0a_barcode_maps.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n\nLints for rule ilmn_1a_merge_fastqs (line 2, /tmp/tmpayc_xtqd/rules/short_read/1a_mergefqs.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n\nLints for rule ilmn_1b_R1_hardTrimming (line 136, /tmp/tmpayc_xtqd/rules/short_read/1b_trimming.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ilmn_1b_R1_internalTrimming (line 170, /tmp/tmpayc_xtqd/rules/short_read/1b_trimming.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ilmn_1c_fastQC_preTrim (line 5, /tmp/tmpayc_xtqd/rules/short_read/1c_fastqc.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule ilmn_1c_fastQC_postTrim (line 30, /tmp/tmpayc_xtqd/rules/short_read/1c_fastqc.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule ilmn_1c_fastQC_twiceTrim (line 54, /tmp/tmpayc_xtqd/rules/short_read/1c_fastqc.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule ilmn_2a_bwa_rRNA_filter_R1 (line 60, /tmp/tmpayc_xtqd/rules/short_read/2a_rRNA_bwa.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ilmn_2a_bwa_rRNA_compress_unmapped (line 82, /tmp/tmpayc_xtqd/rules/short_read/2a_rRNA_bwa.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ilmn_2a_bwa_rRNA_filtered_fastqc (line 99, /tmp/tmpayc_xtqd/rules/short_read/2a_rRNA_bwa.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule ilmn_2b_STAR_rRNA_align (line 7, /tmp/tmpayc_xtqd/rules/short_read/2b_rRNA_STAR.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n\nLints for rule ilmn_2b_STAR_rRNA_compress_outs (line 63, /tmp/tmpayc_xtqd/rules/short_read/2b_rRNA_STAR.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n * Param GENEDIR is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule ilmn_2b_STAR_rRNA_rename_compress_unmapped (line 99, /tmp/tmpayc_xtqd/rules/short_read/2b_rRNA_STAR.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n\nLints for rule ilmn_2b_STAR_rRNA_filtered_fastqc (line 122, /tmp/tmpayc_xtqd/rules/short_read/2b_rRNA_STAR.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule ilmn_2c_qualimapQC_rRNA_STAR (line 37, /tmp/tmpayc_xtqd/rules/short_read/2c_rRNA_qualimap.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule ilmn_2c_qualimap_summary2csv_rRNA_STAR (line 66, /tmp/tmpayc_xtqd/rules/short_read/2c_rRNA_qualimap.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ilmn_2d_ribodetector_get_noRibo_list (line 40, /tmp/tmpayc_xtqd/rules/short_read/2d_ribodetector.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ilmn_2d_ribodetector_gunzip_R1 (line 54, /tmp/tmpayc_xtqd/rules/short_read/2d_ribodetector.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ilmn_2d_ribodetector_filter_R1 (line 66, /tmp/tmpayc_xtqd/rules/short_read/2d_ribodetector.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ilmn_2d_ribodetector_filter_R1_internalTrim (line 82, /tmp/tmpayc_xtqd/rules/short_read/2d_ribodetector.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ilmn_2d_ribodetector_filter_R1_hardTrim (line 98, /tmp/tmpayc_xtqd/rules/short_read/2d_ribodetector.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ilmn_2d_ribodetector_compress_fqs (line 114, /tmp/tmpayc_xtqd/rules/short_read/2d_ribodetector.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ilmn_3a_STARsolo_align (line 9, /tmp/tmpayc_xtqd/rules/short_read/3a_star_align.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n\nLints for rule ilmn_3a_compress_STAR_outs (line 68, /tmp/tmpayc_xtqd/rules/short_read/3a_star_align.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n * Param VELDIR is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param GENEDIR is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param GENEFULLDIR is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule ilmn_3b_fastqc_unmapped (line 7, /tmp/tmpayc_xtqd/rules/short_read/3b_star_unmapped.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule ilmn_3c_strand_split_dedup_bam (line 30, /tmp/tmpayc_xtqd/rules/short_read/3c_star_dedup.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ilmn_3d_qualimapQC_STAR (line 3, /tmp/tmpayc_xtqd/rules/short_read/3d_star_qualimap.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule ilmn_3d_qualimap_summary2csv_STAR (line 31, /tmp/tmpayc_xtqd/rules/short_read/3d_star_qualimap.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ilmn_4a_kbpython_std_remove_suffix (line 65, /tmp/tmpayc_xtqd/rules/short_read/4a_kbpython.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule kbpython_std_compress_outs (line 81, /tmp/tmpayc_xtqd/rules/short_read/4a_kbpython.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ont_1a_merge_formats (line 5, /tmp/tmpayc_xtqd/rules/ont/1a_preprocessing.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ont_1a_readIDs_by_adapter_type (line 102, /tmp/tmpayc_xtqd/rules/ont/1a_preprocessing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ont_1a_adapter_scan_results (line 126, /tmp/tmpayc_xtqd/rules/ont/1a_preprocessing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ont_1a_merge_scan_lists (line 148, /tmp/tmpayc_xtqd/rules/ont/1a_preprocessing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ont_1a_subset_fastq_by_adapter_type (line 165, /tmp/tmpayc_xtqd/rules/ont/1a_preprocessing.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ont_1a_compress_merged_fq (line 194, /tmp/tmpayc_xtqd/rules/ont/1a_preprocessing.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ont_1b_R1_hardTrimming (line 79, /tmp/tmpayc_xtqd/rules/ont/1b_trimming.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ont_1b_R1_internalTrim (line 109, /tmp/tmpayc_xtqd/rules/ont/1b_trimming.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ont_1c_fastq_call_bc_from_adapter (line 3, /tmp/tmpayc_xtqd/rules/ont/1c_barcode_calling.smk):\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n\nLints for rule ont_1c_filter_read_barcodes (line 64, /tmp/tmpayc_xtqd/rules/ont/1c_barcode_calling.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ont_1c_tsv_bc_correction (line 79, /tmp/tmpayc_xtqd/rules/ont/1c_barcode_calling.smk):\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n\nLints for rule ont_1d_sort_compress_output (line 45, /tmp/tmpayc_xtqd/rules/ont/1d_minimap2.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ont_1d_add_featureCounts_to_bam (line 137, /tmp/tmpayc_xtqd/rules/ont/1d_minimap2.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ont_1d_add_corrected_barcodes (line 166, /tmp/tmpayc_xtqd/rules/ont/1d_minimap2.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ont_1d_add_umis (line 194, /tmp/tmpayc_xtqd/rules/ont/1d_minimap2.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ont_1d_filter_bam_empty_tags (line 222, /tmp/tmpayc_xtqd/rules/ont/1d_minimap2.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ont_1d_counts_to_sparse (line 278, /tmp/tmpayc_xtqd/rules/ont/1d_minimap2.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule ont_clipBeforeSTAR (line 4, /tmp/tmpayc_xtqd/rules/ont/1d_STAR.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule ont_STARsolo_align (line 27, /tmp/tmpayc_xtqd/rules/ont/1d_STAR.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n\nLints for rule ont_compress_STAR_outs (line 119, /tmp/tmpayc_xtqd/rules/ont/1d_STAR.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Migrate long run directives into scripts or notebooks:\n Long run directives hamper workflow readability. Use the script or\n notebook directive instead. Note that the script or notebook directive\n does not involve boilerplate. Similar to run, you will have direct access\n to params, input, output, and wildcards.Only use the run directive for a\n handful of lines.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#external-scripts\n https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#jupyter-notebook-integration\n * Param VELDIR is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n * Param GENEFULLDIR is a prefix of input or output file but hardcoded:\n If this is meant to represent a file path prefix, it will fail when\n running workflow in environments without a shared filesystem. Instead,\n provide a function that infers the appropriate prefix from the input or\n output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules\n https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions\n\nLints for rule ont_2_qualimap_minimap2 (line 2, /tmp/tmpayc_xtqd/rules/ont/2_qualimap.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule ont_2_qualimap_STAR (line 31, /tmp/tmpayc_xtqd/rules/ont/2_qualimap.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule ont_2_qualimap_summary2csv (line 60, /tmp/tmpayc_xtqd/rules/ont/2_qualimap.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ont_readQC_0_rawInput (line 2, /tmp/tmpayc_xtqd/rules/ont/2_read_qc.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ont_readQC_1_preCutadapt (line 26, /tmp/tmpayc_xtqd/rules/ont/2_read_qc.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ont_readQC_2_postCutadapt (line 50, /tmp/tmpayc_xtqd/rules/ont/2_read_qc.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ont_readQC_3_bam (line 89, /tmp/tmpayc_xtqd/rules/ont/2_read_qc.smk):\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule readQC_downsample (line 116, /tmp/tmpayc_xtqd/rules/ont/2_read_qc.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule ont_readQC_summaryplot (line 133, /tmp/tmpayc_xtqd/rules/ont/2_read_qc.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule ont_fastQC_preTrim (line 2, /tmp/tmpayc_xtqd/rules/ont/2_fastqc.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule ont_fastQC_preCutadapt (line 25, /tmp/tmpayc_xtqd/rules/ont/2_fastqc.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule ont_fastQC_postCutadapt (line 48, /tmp/tmpayc_xtqd/rules/ont/2_fastqc.smk):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 4, + "subscribers_count": 3, + "topics": [], + "updated_at": 1726929831.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": "Cut And Run Analysis Pipeline", + "formatting": "[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\s\u0027\n[DEBUG] In file \"/tmp/tmpr72wxess/CCBR-CARLISLE-0b1e117/workflow/rules/annotations.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpr72wxess/CCBR-CARLISLE-0b1e117/workflow/rules/align.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmpr72wxess/CCBR-CARLISLE-0b1e117/workflow/rules/init.smk\": NoParametersError: L354: In input definition.\n[DEBUG] In file \"/tmp/tmpr72wxess/CCBR-CARLISLE-0b1e117/workflow/rules/init.smk\": \n[DEBUG] In file \"/tmp/tmpr72wxess/CCBR-CARLISLE-0b1e117/workflow/rules/peakcalls.smk\": Formatted content is different from original\n[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\s\u0027\n[DEBUG] In file \"/tmp/tmpr72wxess/CCBR-CARLISLE-0b1e117/workflow/rules/qc.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpr72wxess/CCBR-CARLISLE-0b1e117/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpr72wxess/CCBR-CARLISLE-0b1e117/workflow/rules/diff.smk\": Formatted content is different from original\n[INFO] 1 file(s) raised parsing errors \ud83e\udd15\n[INFO] 6 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "CCBR/CARLISLE", + "latest_release": "v2.6.0", + "linting": "IndexError in file /tmp/tmpr72wxess/CCBR-CARLISLE-0b1e117/workflow/rules/init.smk, line 43:\nlist index out of range\n File \"/tmp/tmpr72wxess/CCBR-CARLISLE-0b1e117/workflow/rules/init.smk\", line 43, in \u003cmodule\u003e\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 4, + "subscribers_count": 5, + "topics": [ + "pipeline", + "workflow" + ], + "updated_at": 1726843286.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": null, + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpl34ftw0e/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "NeLLi-team/gvclass", + "latest_release": null, + "linting": "KeyError in file /tmp/tmpl34ftw0e/workflow/Snakefile, line 45:\n\u0027querydir\u0027\n File \"/tmp/tmpl34ftw0e/workflow/Snakefile\", line 45, in \u003cmodule\u003e\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 4, + "subscribers_count": 3, + "topics": [], + "updated_at": 1726785430.0 + }, + { + "config_readme": "\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eGeneral settings\u003c/h1\u003e\u003ca id=\"user-content-general-settings\" class=\"anchor\" aria-label=\"Permalink: General settings\" href=\"#general-settings\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eTo configure this workflow, modify \u003ccode\u003econfig/config.yaml\u003c/code\u003e according to your needs, following the explanations provided in the file.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eSample sheet\u003c/h1\u003e\u003ca id=\"user-content-sample-sheet\" class=\"anchor\" aria-label=\"Permalink: Sample sheet\" href=\"#sample-sheet\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eAdd samples to \u003ccode\u003econfig/samples.tsv\u003c/code\u003e. For each sample, the columns \u003ccode\u003esample_name\u003c/code\u003e, \u003ccode\u003ealias\u003c/code\u003e, \u003ccode\u003eplatform\u003c/code\u003e, and \u003ccode\u003egroup\u003c/code\u003e have to be defined.\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003eSamples within the same \u003ccode\u003egroup\u003c/code\u003e will be called jointly.\u003c/li\u003e\n\u003cli\u003eAliases represent the name of the sample within its group (they can be the same as the sample name, or something simpler, e.g. tumor or normal).\u003c/li\u003e\n\u003cli\u003eThe \u003ccode\u003eplatform\u003c/code\u003e column needs to contain the used sequencing plaform (one of \u0027CAPILLARY\u0027, \u0027LS454\u0027, \u0027ILLUMINA\u0027, \u0027SOLID\u0027, \u0027HELICOS\u0027, \u0027IONTORRENT\u0027, \u0027ONT\u0027, \u0027PACBIO\u2019).\u003c/li\u003e\n\u003cli\u003eThe \u003ccode\u003effpe\u003c/code\u003e column specifies whether a sample is a ffpe substrate (1) or not (0). ffpe treated normal samples are not supported.\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eMissing values can be specified by empty columns or by writing \u003ccode\u003eNA\u003c/code\u003e. Lines can be commented out with \u003ccode\u003e#\u003c/code\u003e.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eUnit sheet\u003c/h1\u003e\u003ca id=\"user-content-unit-sheet\" class=\"anchor\" aria-label=\"Permalink: Unit sheet\" href=\"#unit-sheet\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eFor each sample, add one or more sequencing units (runs, lanes or replicates) to the unit sheet \u003ccode\u003econfig/units.tsv\u003c/code\u003e.\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003eEach unit has a \u003ccode\u003eunit_name\u003c/code\u003e, which can be e.g. a running number, or an actual run, lane or replicate id.\u003c/li\u003e\n\u003cli\u003eEach unit has a \u003ccode\u003esample_name\u003c/code\u003e, which associates it with the biological sample it comes from.\u003c/li\u003e\n\u003cli\u003eFor each unit, define either one (column \u003ccode\u003efq1\u003c/code\u003e) or two (columns \u003ccode\u003efq1\u003c/code\u003e, \u003ccode\u003efq2\u003c/code\u003e) FASTQ files (these can point to anywhere in your system).\u003c/li\u003e\n\u003cli\u003eAlternatively, you can define an SRA (sequence read archive) accession (starting with e.g. ERR or SRR) by using a column \u003ccode\u003esra\u003c/code\u003e. In the latter case, the pipeline will automatically download the corresponding paired end reads from SRA. If both local files and SRA accession are available, the local files will be preferred.\u003c/li\u003e\n\u003cli\u003eDefine adapters in the \u003ccode\u003eadapters\u003c/code\u003e column, by putting \u003ca href=\"https://cutadapt.readthedocs.org\" rel=\"nofollow\"\u003ecutadapt arguments\u003c/a\u003e in quotation marks (e.g. \u003ccode\u003e\"-a ACGCGATCG -A GCTAGCGTACT\"\u003c/code\u003e).\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eMissing values can be specified by empty columns or by writing \u003ccode\u003eNA\u003c/code\u003e. Lines can be commented out with \u003ccode\u003e#\u003c/code\u003e.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003ePrimer trimming\u003c/h1\u003e\u003ca id=\"user-content-primer-trimming\" class=\"anchor\" aria-label=\"Permalink: Primer trimming\" href=\"#primer-trimming\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eFor panel data the pipeline allows trimming of amplicon primers on both ends of a fragment but also on a single end only.\nIn case of single end primers these are supposed to be located at the left end of a read.\nWhen primer trimming is enabled, primers have to be defined either directly in the \u003ccode\u003econfig.yaml\u003c/code\u003e or in a seperate tsv-file.\nDefining primers directly in the config file is prefered when all samples come from the same primer set.\nIn case of different panels, primers have to be set panel-wise in a seperate tsv-file (the path to that tsv can be set in the config under \u003ccode\u003eprimers/trimming/tsv\u003c/code\u003e).\nFor each panel the following columns need to be set: \u003ccode\u003epanel\u003c/code\u003e, \u003ccode\u003efa1\u003c/code\u003e and \u003ccode\u003efa2\u003c/code\u003e (optional).\nAdditionally, for each sample the corresponding panel must be defined in \u003ccode\u003esamples.tsv\u003c/code\u003e (column \u003ccode\u003epanel\u003c/code\u003e).\nFor single primer trimming only, the first entry in the config (respective in the tsv file) needs to be defined.\u003c/p\u003e\n", + "data_format": 2, + "description": "A flavor of https://github.com/snakemake-workflows/dna-seq-varlociraptor preconfigured for molecular tumor boards", + "formatting": null, + "full_name": "snakemake-workflows/dna-seq-mtb", + "latest_release": "v1.8.0", + "linting": null, + "mandatory_flags": null, + "report": true, + "software_stack_deployment": { + "conda": true, + "singularity": false, + "singularity+conda": false + }, + "standardized": true, + "stargazers_count": 4, + "subscribers_count": 2, + "topics": [], + "updated_at": 1721205075.0 + }, { "config_readme": "\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eWorkflow configuration\u003c/h1\u003e\u003ca id=\"user-content-workflow-configuration\" class=\"anchor\" aria-label=\"Permalink: Workflow configuration\" href=\"#workflow-configuration\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eConfiguration\u003c/h2\u003e\u003ca id=\"user-content-configuration\" class=\"anchor\" aria-label=\"Permalink: Configuration\" href=\"#configuration\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eTo configure the workflow, modifiy \u003ccode\u003econfig/config.yaml\u003c/code\u003e according\nto your needs.\u003c/p\u003e\n\u003cp\u003eFor specific details about the parameters\ncheck the documentation.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003eOptimized configuration for 16S birds and mammals metabarcoding\u003c/h3\u003e\u003ca id=\"user-content-optimized-configuration-for-16s-birds-and-mammals-metabarcoding\" class=\"anchor\" aria-label=\"Permalink: Optimized configuration for 16S birds and mammals metabarcoding\" href=\"#optimized-configuration-for-16s-birds-and-mammals-metabarcoding\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eA configuration file with optimized parameters (with no warranty!) for\nthe analysis of 16S metabarcoding experiments of birds and mammals is\nincluded in this folder.\n\u003cstrong\u003eYou will still need to modify the indicated paths to match your own folder structure.\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eSee for reference:\u003c/p\u003e\n\u003cp\u003eDenay, G.; Preckel, L.; Petersen, H.; Pietsch, K.; W\u00f6hlke, A.; Br\u00fcnen-Nieweler, C.\nBenchmarking and Validation of a Bioinformatics Workflow for Meat Species Identification Using 16S rDNA Metabarcoding.\nFoods 2023, 12, 968. \u003ca href=\"https://doi.org/10.3390/foods12050968\" rel=\"nofollow\"\u003ehttps://doi.org/10.3390/foods12050968\u003c/a\u003e\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eSample sheet\u003c/h2\u003e\u003ca id=\"user-content-sample-sheet\" class=\"anchor\" aria-label=\"Permalink: Sample sheet\" href=\"#sample-sheet\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eAdd your samples to \u003ccode\u003econfig/samples.tsv\u003c/code\u003e or use the\nthe helper script from Bundes Insitut f\u00fcr Risikobewertung in\n\u003ccode\u003eressources/creat_sampleSheet.sh\u003c/code\u003e.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eReference table\u003c/h2\u003e\u003ca id=\"user-content-reference-table\" class=\"anchor\" aria-label=\"Permalink: Reference table\" href=\"#reference-table\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eIf using the benchmark mode, sdd information for your reference samples in the \u003ccode\u003ereference.tsv\u003c/code\u003e template.\nNote that proportions are given as fractions in the [0, 1] interval.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eParameter space exploration configuration\u003c/h2\u003e\u003ca id=\"user-content-parameter-space-exploration-configuration\" class=\"anchor\" aria-label=\"Permalink: Parameter space exploration configuration\" href=\"#parameter-space-exploration-configuration\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eTo configure a parameter space exploration analysis, modify the file\n\u003ccode\u003econfig_paramspace.yaml\u003c/code\u003e according to your needs.\u003c/p\u003e\n\u003cp\u003eFor specific details about the parameters\ncheck the documentation.\u003c/p\u003e\n", "data_format": 2, @@ -50726,6 +50726,30 @@ var data = "topics": [], "updated_at": 1604895310.0 }, + { + "config_readme": null, + "data_format": 2, + "description": "gNOMO2 allows integrated multi-omics analyses of microbiomes", + "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmpjj6yy_l1/workflow/rules/Module4.smk\": InvalidPython: Black error:\n```\nCannot parse: 13:0: \u003cline number missing in source\u003e\n```\n\n[DEBUG] In file \"/tmp/tmpjj6yy_l1/workflow/rules/Module4.smk\": \n[ERROR] In file \"/tmp/tmpjj6yy_l1/workflow/rules/Module2.smk\": InvalidPython: Black error:\n```\nCannot parse: 12:0: \u003cline number missing in source\u003e\n```\n\n[DEBUG] In file \"/tmp/tmpjj6yy_l1/workflow/rules/Module2.smk\": \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\s\u0027\n[DEBUG] In file \"/tmp/tmpjj6yy_l1/workflow/rules/MT_PE.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpjj6yy_l1/workflow/rules/Module3.smk\": Formatted content is different from original\n[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\.\u0027\n[DEBUG] In file \"/tmp/tmpjj6yy_l1/workflow/rules/MP.smk\": Formatted content is different from original\n[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\s\u0027\n[DEBUG] In file \"/tmp/tmpjj6yy_l1/workflow/rules/MG.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpjj6yy_l1/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\[\u0027\n[DEBUG] In file \"/tmp/tmpjj6yy_l1/workflow/rules/AS_SE.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmpjj6yy_l1/workflow/rules/Module5.smk\": InvalidPython: Black error:\n```\nCannot parse: 13:0: \u003cline number missing in source\u003e\n```\n\n[DEBUG] In file \"/tmp/tmpjj6yy_l1/workflow/rules/Module5.smk\": \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\[\u0027\n[DEBUG] In file \"/tmp/tmpjj6yy_l1/workflow/rules/AS_PE.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmpjj6yy_l1/workflow/rules/Module6.smk\": InvalidPython: Black error:\n```\nCannot parse: 14:0: \u003cline number missing in source\u003e\n```\n\n[DEBUG] In file \"/tmp/tmpjj6yy_l1/workflow/rules/Module6.smk\": \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\s\u0027\n[DEBUG] In file \"/tmp/tmpjj6yy_l1/workflow/rules/MT_SE.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpjj6yy_l1/workflow/rules/Module1.smk\": Formatted content is different from original\n[INFO] 4 file(s) raised parsing errors \ud83e\udd15\n[INFO] 9 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "muzafferarikan/gNOMO2", + "latest_release": null, + "linting": "Traceback (most recent call last):\n\n File \"/tmp/tmpjj6yy_l1/workflow/Snakefile\", line 7, in \u003cmodule\u003e\n pkg_resources.require(f\"snakemake=={required_version}\")\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pkg_resources/__init__.py\", line 1069, in require\n needed = self.resolve(parse_requirements(requirements))\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pkg_resources/__init__.py\", line 896, in resolve\n dist = self._resolve_dist(\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pkg_resources/__init__.py\", line 942, in _resolve_dist\n raise VersionConflict(dist, req).with_context(dependent_req)\n\npkg_resources.VersionConflict: (snakemake 8.16.0 (/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages), Requirement.parse(\u0027snakemake==7.15.2\u0027))\n\n\nDuring handling of the above exception, another exception occurred:\n\n\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpjj6yy_l1/workflow/Snakefile\", line 9, in \u003cmodule\u003e\n raise ImportError(f\"Snakemake version {required_version} is required.\")\n\nImportError: Snakemake version 7.15.2 is required.\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 5, + "subscribers_count": 2, + "topics": [ + "amplicon-sequencing", + "metagenomics", + "metaproteomics", + "metatranscriptomics", + "microbiome", + "multi-omics" + ], + "updated_at": 1723038005.0 + }, { "config_readme": null, "data_format": 2, @@ -50753,30 +50777,6 @@ var data = ], "updated_at": 1725437754.0 }, - { - "config_readme": null, - "data_format": 2, - "description": "gNOMO2 allows integrated multi-omics analyses of microbiomes", - "formatting": "[DEBUG] \n[ERROR] In file \"/tmp/tmpjj6yy_l1/workflow/rules/Module4.smk\": InvalidPython: Black error:\n```\nCannot parse: 13:0: \u003cline number missing in source\u003e\n```\n\n[DEBUG] In file \"/tmp/tmpjj6yy_l1/workflow/rules/Module4.smk\": \n[ERROR] In file \"/tmp/tmpjj6yy_l1/workflow/rules/Module2.smk\": InvalidPython: Black error:\n```\nCannot parse: 12:0: \u003cline number missing in source\u003e\n```\n\n[DEBUG] In file \"/tmp/tmpjj6yy_l1/workflow/rules/Module2.smk\": \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\s\u0027\n[DEBUG] In file \"/tmp/tmpjj6yy_l1/workflow/rules/MT_PE.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpjj6yy_l1/workflow/rules/Module3.smk\": Formatted content is different from original\n[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\.\u0027\n[DEBUG] In file \"/tmp/tmpjj6yy_l1/workflow/rules/MP.smk\": Formatted content is different from original\n[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\s\u0027\n[DEBUG] In file \"/tmp/tmpjj6yy_l1/workflow/rules/MG.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpjj6yy_l1/workflow/Snakefile\": Formatted content is different from original\n[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\[\u0027\n[DEBUG] In file \"/tmp/tmpjj6yy_l1/workflow/rules/AS_SE.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmpjj6yy_l1/workflow/rules/Module5.smk\": InvalidPython: Black error:\n```\nCannot parse: 13:0: \u003cline number missing in source\u003e\n```\n\n[DEBUG] In file \"/tmp/tmpjj6yy_l1/workflow/rules/Module5.smk\": \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\[\u0027\n[DEBUG] In file \"/tmp/tmpjj6yy_l1/workflow/rules/AS_PE.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmpjj6yy_l1/workflow/rules/Module6.smk\": InvalidPython: Black error:\n```\nCannot parse: 14:0: \u003cline number missing in source\u003e\n```\n\n[DEBUG] In file \"/tmp/tmpjj6yy_l1/workflow/rules/Module6.smk\": \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\s\u0027\n[DEBUG] In file \"/tmp/tmpjj6yy_l1/workflow/rules/MT_SE.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmpjj6yy_l1/workflow/rules/Module1.smk\": Formatted content is different from original\n[INFO] 4 file(s) raised parsing errors \ud83e\udd15\n[INFO] 9 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "muzafferarikan/gNOMO2", - "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/tmp/tmpjj6yy_l1/workflow/Snakefile\", line 7, in \u003cmodule\u003e\n pkg_resources.require(f\"snakemake=={required_version}\")\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pkg_resources/__init__.py\", line 1069, in require\n needed = self.resolve(parse_requirements(requirements))\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pkg_resources/__init__.py\", line 896, in resolve\n dist = self._resolve_dist(\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/pkg_resources/__init__.py\", line 942, in _resolve_dist\n raise VersionConflict(dist, req).with_context(dependent_req)\n\npkg_resources.VersionConflict: (snakemake 8.16.0 (/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages), Requirement.parse(\u0027snakemake==7.15.2\u0027))\n\n\nDuring handling of the above exception, another exception occurred:\n\n\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpjj6yy_l1/workflow/Snakefile\", line 9, in \u003cmodule\u003e\n raise ImportError(f\"Snakemake version {required_version} is required.\")\n\nImportError: Snakemake version 7.15.2 is required.\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 5, - "subscribers_count": 2, - "topics": [ - "amplicon-sequencing", - "metagenomics", - "metaproteomics", - "metatranscriptomics", - "microbiome", - "multi-omics" - ], - "updated_at": 1723038005.0 - }, { "config_readme": null, "data_format": 2, @@ -51423,6 +51423,23 @@ var data = ], "updated_at": 1602644548.0 }, + { + "config_readme": null, + "data_format": 2, + "description": "Bisulphite-sequencing based methylation pipeline", + "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmpo885rykl/OpenOmics-methyl-seek-cc74d7c/Snakefile\": Keyword \"input\" at line 171 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\$\u0027\n[WARNING] In file \"/tmp/tmpo885rykl/OpenOmics-methyl-seek-cc74d7c/Snakefile\": Keyword \"output\" at line 802 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpo885rykl/OpenOmics-methyl-seek-cc74d7c/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "OpenOmics/methyl-seek", + "latest_release": "v1.0.0", + "linting": "/tmp/tmpo885rykl/OpenOmics-methyl-seek-cc74d7c/Snakefile:456: SyntaxWarning: invalid escape sequence \u0027\\$\u0027\n cd {params.dir}\n/tmp/tmpo885rykl/OpenOmics-methyl-seek-cc74d7c/Snakefile:488: SyntaxWarning: invalid escape sequence \u0027\\$\u0027\n out2=join(working_dir,\"rseqc/{samples}.Rdist.info\")\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpo885rykl/OpenOmics-methyl-seek-cc74d7c/Snakefile\", line 16, in \u003cmodule\u003e\n sample_file= config[\"samples\"]\n ~~~~~^^^^^^^^^^^^\n\nKeyError: \u0027samples\u0027\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 6, + "subscribers_count": 2, + "topics": [], + "updated_at": 1723560372.0 + }, { "config_readme": "\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eDependencies installation\u003c/h1\u003e\u003ca id=\"user-content-dependencies-installation\" class=\"anchor\" aria-label=\"Permalink: Dependencies installation\" href=\"#dependencies-installation\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eCreate and activate the virtual environment with the required dependencies\nwith Conda:\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-shell\"\u003e\u003cpre\u003econda env create -f environment.yml\nconda activate mirflowz\u003c/pre\u003e\u003c/div\u003e\n\u003cp\u003eIf you plan to run \u003cem\u003eMIRFLOWZ\u003c/em\u003e via Conda, we recommend using the following\ncommand for a faster environment creation, specially if you will run it on an\nHPC cluster.\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-shell\"\u003e\u003cpre\u003econda config --set channel_priority strict\u003c/pre\u003e\u003c/div\u003e\n\u003cp\u003eFor a faster creation of the environment (and Conda environments in general),\nyou can also install \u003ca href=\"https://github.com/mamba-org/mamba\"\u003eMamba\u003c/a\u003e on top of Conda. In that case, replace\n\u003ccode\u003econda\u003c/code\u003e with \u003ccode\u003emamba\u003c/code\u003e in the commands above (particularly in\n\u003ccode\u003econda env create\u003c/code\u003e).\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eRunning \u003cem\u003eMIRFLOWZ\u003c/em\u003e with Singularity\u003c/h2\u003e\u003ca id=\"user-content-running-mirflowz-with-singularity\" class=\"anchor\" aria-label=\"Permalink: Running MIRFLOWZ with Singularity\" href=\"#running-mirflowz-with-singularity\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eIf you want to run \u003cem\u003eMIRFLOWZ\u003c/em\u003e via Singularity and do not already\nhave it installed globally on your system, you must further update the Conda\nenvironment with:\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-shell\"\u003e\u003cpre\u003econda env update -f environment.root.yml\u003c/pre\u003e\u003c/div\u003e\n\u003cblockquote\u003e\n\u003cp\u003eMind that you must have the environment activated and root permissions on\nyour system to install Singularity. If you want to run \u003cem\u003eMIRFLOWZ\u003c/em\u003e on an HPC\ncluster (recommended in almost all cases), ask your system administrator\nabout Singularity.\u003c/p\u003e\n\u003c/blockquote\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eRun the workflow on your own samples\u003c/h1\u003e\u003ca id=\"user-content-run-the-workflow-on-your-own-samples\" class=\"anchor\" aria-label=\"Permalink: Run the workflow on your own samples\" href=\"#run-the-workflow-on-your-own-samples\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eIn order to run \u003cem\u003eMIRFLOWZ\u003c/em\u003e on your own samples, we recommend having all the\ninput files inside a dedicated directory. This way, it is easier to keep the\ndata together and reproduce an analysis. Assuming that your current directory\nis the repository\u0027s root directory, create a directory to store all your data\nand traverse to it with:\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-shell\"\u003e\u003cpre\u003emkdir path/to/your_run\n\u003cspan class=\"pl-c1\"\u003ecd\u003c/span\u003e path/to/your_run\u003c/pre\u003e\u003c/div\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003e1. Prepare the sample table\u003c/h2\u003e\u003ca id=\"user-content-1-prepare-the-sample-table\" class=\"anchor\" aria-label=\"Permalink: 1. Prepare the sample table\" href=\"#1-prepare-the-sample-table\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eCreate an empty sample table. Refer to the\n\u003ca href=\"../test/test_files/samples_table.tsv\"\u003esample.tsv\u003c/a\u003e test file to see what the\ntable must look like or use it as a template.\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-shell\"\u003e\u003cpre\u003etouch samples.tsv\u003c/pre\u003e\u003c/div\u003e\n\u003cblockquote\u003e\n\u003cp\u003eFill the sample table according to the following requirements:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003e\n\u003ccode\u003esample\u003c/code\u003e. Arbitrary name for the miRNA sequencing library.\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003esample_file\u003c/code\u003e. Path to the miRNA sequencing library file. The path must be\nrelative to the directory where the workflow will be run.\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003eadapter\u003c/code\u003e. Sequence of the 3\u0027-end adapter used during library preparation.\u003c/li\u003e\n\u003cli\u003e\n\u003ccode\u003eformat\u003c/code\u003e. One of \u003ccode\u003efa\u003c/code\u003e/\u003ccode\u003efasta\u003c/code\u003e or \u003ccode\u003efq\u003c/code\u003e/\u003ccode\u003efastq\u003c/code\u003e, if the library file is in\nFASTA or FASTQ format, respectively.\u003c/li\u003e\n\u003c/ul\u003e\n\u003c/blockquote\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003e2. Prepare the genome resources\u003c/h2\u003e\u003ca id=\"user-content-2-prepare-the-genome-resources\" class=\"anchor\" aria-label=\"Permalink: 2. Prepare the genome resources\" href=\"#2-prepare-the-genome-resources\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThere are 4 files you must provide:\u003c/p\u003e\n\u003col\u003e\n\u003cli\u003e\n\u003cp\u003eA \u003cstrong\u003e\u003ccode\u003egzip\u003c/code\u003eped FASTA\u003c/strong\u003e file containing \u003cstrong\u003ereference sequences\u003c/strong\u003e, typically the\ngenome of the source/organism from which the library was extracted.\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003eA \u003cstrong\u003e\u003ccode\u003egzip\u003c/code\u003eped GTF\u003c/strong\u003e file with matching \u003cstrong\u003egene annotations\u003c/strong\u003e for the\nreference sequences above.\u003c/p\u003e\n\u003c/li\u003e\n\u003c/ol\u003e\n\u003cblockquote\u003e\n\u003cp\u003e\u003cem\u003eMIRFLOWZ\u003c/em\u003e expects both the reference sequence and gene annotation files to\nfollow \u003ca href=\"https://ensembl.org/\" rel=\"nofollow\"\u003eEnsembl\u003c/a\u003e style/formatting. If you obtained these files from\na source other than Ensembl, you must ensure that they adhere to the\nexpected format by converting them, if necessary.\u003c/p\u003e\n\u003c/blockquote\u003e\n\u003col start=\"3\"\u003e\n\u003cli\u003eAn \u003cstrong\u003euncompressed GFF3\u003c/strong\u003e file with \u003cstrong\u003emicroRNA annotations\u003c/strong\u003e for the reference\nsequences above.\u003c/li\u003e\n\u003c/ol\u003e\n\u003cblockquote\u003e\n\u003cp\u003e\u003cem\u003eMIRFLOWZ\u003c/em\u003e expects the miRNA annotations to follow \u003ca href=\"https://mirbase.org/\" rel=\"nofollow\"\u003emiRBase\u003c/a\u003e\nstyle/formatting. If you obtained this file from a source other than miRBase,\nyou must ensure that it adheres to the expected format by converting it, if\nnecessary.\u003c/p\u003e\n\u003c/blockquote\u003e\n\u003col start=\"4\"\u003e\n\u003cli\u003e\n\u003cp\u003eAn \u003cstrong\u003euncompressed tab-separated file\u003c/strong\u003e with a \u003cstrong\u003emapping between the\nreference names\u003c/strong\u003e used in the miRNA annotation file (column 1; \"UCSC style\")\nand in the gene annotations and reference sequence files (column 2; \"Ensembl\nstyle\"). Values in column 1 are expected to be unique, no header is\nexpected, and any additional columns will be ignored. \u003ca href=\"https://github.com/dpryan79/ChromosomeMappings\"\u003eThis\nresource\u003c/a\u003e provides such files for various organisms, and in the\nexpected format.\u003c/p\u003e\n\u003c/li\u003e\n\u003cli\u003e\n\u003cp\u003e\u003cstrong\u003eOPTIONAL\u003c/strong\u003e: A \u003cstrong\u003eBED6\u003c/strong\u003e file with regions for which to produce\n\u003ca href=\"https://git.scicore.unibas.ch/zavolan_group/tools/ascii-alignment-pileup\" rel=\"nofollow\"\u003eASCII-style alignment pileups\u003c/a\u003e. If not provided, no pileups\nwill be generated. See \u003ca href=\"https://gist.github.com/deliaBlue/19ad3740c95937378bd9281bd9d1bc72\"\u003ehere\u003c/a\u003e for the expected format.\u003c/p\u003e\n\u003c/li\u003e\n\u003c/ol\u003e\n\u003cblockquote\u003e\n\u003cp\u003eGeneral note: If you want to process the genome resources before use (e.g.,\nfiltering), you can do that, but make sure the formats of any modified\nresource files meet the formatting expectations outlined above!\u003c/p\u003e\n\u003c/blockquote\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003e3. Prepare the configuration file\u003c/h2\u003e\u003ca id=\"user-content-3-prepare-the-configuration-file\" class=\"anchor\" aria-label=\"Permalink: 3. Prepare the configuration file\" href=\"#3-prepare-the-configuration-file\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eWe recommend creating a copy of the\n\u003ca href=\"config_template.yaml\"\u003econfiguration file template\u003c/a\u003e.\u003c/p\u003e\n\u003cdiv class=\"highlight highlight-source-shell\"\u003e\u003cpre\u003ecp ../config/config_template.yaml config.yaml\n\u003c/pre\u003e\u003c/div\u003e\n\u003cp\u003eOpen the new copy in your editor of choice and adjust the configuration\nparameters to your liking. The template explains what each of the parameters\nmean and how you can meaningfully adjust them.\u003c/p\u003e\n", "data_format": 2, @@ -51539,23 +51556,6 @@ var data = "topics": [], "updated_at": 1726651498.0 }, - { - "config_readme": null, - "data_format": 2, - "description": "Bisulphite-sequencing based methylation pipeline", - "formatting": "[DEBUG] \n[WARNING] In file \"/tmp/tmpo885rykl/OpenOmics-methyl-seek-cc74d7c/Snakefile\": Keyword \"input\" at line 171 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\$\u0027\n[WARNING] In file \"/tmp/tmpo885rykl/OpenOmics-methyl-seek-cc74d7c/Snakefile\": Keyword \"output\" at line 802 has comments under a value.\n\tPEP8 recommends block comments appear before what they describe\n(see https://www.python.org/dev/peps/pep-0008/#id30)\n[DEBUG] In file \"/tmp/tmpo885rykl/OpenOmics-methyl-seek-cc74d7c/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "OpenOmics/methyl-seek", - "latest_release": "v1.0.0", - "linting": "/tmp/tmpo885rykl/OpenOmics-methyl-seek-cc74d7c/Snakefile:456: SyntaxWarning: invalid escape sequence \u0027\\$\u0027\n cd {params.dir}\n/tmp/tmpo885rykl/OpenOmics-methyl-seek-cc74d7c/Snakefile:488: SyntaxWarning: invalid escape sequence \u0027\\$\u0027\n out2=join(working_dir,\"rseqc/{samples}.Rdist.info\")\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2024, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmpo885rykl/OpenOmics-methyl-seek-cc74d7c/Snakefile\", line 16, in \u003cmodule\u003e\n sample_file= config[\"samples\"]\n ~~~~~^^^^^^^^^^^^\n\nKeyError: \u0027samples\u0027\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 6, - "subscribers_count": 2, - "topics": [], - "updated_at": 1723560372.0 - }, { "config_readme": null, "data_format": 2, @@ -51990,6 +51990,23 @@ var data = "topics": [], "updated_at": 1612269653.0 }, + { + "config_readme": null, + "data_format": 2, + "description": "Generation of OrthoDB protein sets for gene prediction experiments", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp4jzao92t/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "tomasbruna/orthodb-clades", + "latest_release": null, + "linting": "Lints for rule selectBombusSpeciesExcl (line 48, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectBombusOrderExcl (line 74, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectParasteatodaSpeciesExcl (line 98, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectParasteatodaOrderExcl (line 124, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectRhodiusSpeciesExcl (line 148, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectRhodniusOrderExcl (line 174, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectTetraodonSpeciesExcl (line 198, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectTetraodonOrderExcl (line 224, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectDanioSpeciesExcl (line 252, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectDanioOrderExcl (line 278, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectPoplarSpeciesExcl (line 305, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectPoplarOrderExcl (line 331, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectMedicagoSpeciesExcl (line 355, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectMedicagoOrderExcl (line 381, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectTomatoSpeciesExcl (line 405, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectTomatoOrderExcl (line 431, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectChickenSpeciesExcl (line 455, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectChickenOrderExcl (line 481, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectMouseSpeciesExcl (line 509, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectMouseOrderExcl (line 535, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectCelegansSpeciesExcl (line 559, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectCelegansOrderExcl (line 585, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectArabiSpeciesExcl (line 613, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectArabiOrderExcl (line 639, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectDrosophilaSpeciesExcl (line 663, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectDrosophilaOrderExcl (line 689, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectViridiplantae (line 714, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectFungi (line 737, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectVertebrata (line 760, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectMetazoa (line 783, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectArthropoda (line 806, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectEukaryota (line 829, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule unzip (line 854, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule download (line 875, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 7, + "subscribers_count": 2, + "topics": [], + "updated_at": 1725785605.0 + }, { "config_readme": null, "data_format": 2, @@ -52024,23 +52041,6 @@ var data = "topics": [], "updated_at": 1726493544.0 }, - { - "config_readme": null, - "data_format": 2, - "description": "Generation of OrthoDB protein sets for gene prediction experiments", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp4jzao92t/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "tomasbruna/orthodb-clades", - "latest_release": null, - "linting": "Lints for rule selectBombusSpeciesExcl (line 48, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectBombusOrderExcl (line 74, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectParasteatodaSpeciesExcl (line 98, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectParasteatodaOrderExcl (line 124, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectRhodiusSpeciesExcl (line 148, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectRhodniusOrderExcl (line 174, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectTetraodonSpeciesExcl (line 198, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectTetraodonOrderExcl (line 224, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectDanioSpeciesExcl (line 252, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectDanioOrderExcl (line 278, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectPoplarSpeciesExcl (line 305, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectPoplarOrderExcl (line 331, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectMedicagoSpeciesExcl (line 355, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectMedicagoOrderExcl (line 381, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectTomatoSpeciesExcl (line 405, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectTomatoOrderExcl (line 431, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectChickenSpeciesExcl (line 455, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectChickenOrderExcl (line 481, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectMouseSpeciesExcl (line 509, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectMouseOrderExcl (line 535, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectCelegansSpeciesExcl (line 559, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectCelegansOrderExcl (line 585, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectArabiSpeciesExcl (line 613, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectArabiOrderExcl (line 639, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectDrosophilaSpeciesExcl (line 663, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectDrosophilaOrderExcl (line 689, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectViridiplantae (line 714, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectFungi (line 737, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectVertebrata (line 760, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectMetazoa (line 783, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectArthropoda (line 806, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule selectEukaryota (line 829, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule unzip (line 854, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\nLints for rule download (line 875, /tmp/tmp4jzao92t/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 7, - "subscribers_count": 2, - "topics": [], - "updated_at": 1725785605.0 - }, { "config_readme": null, "data_format": 2, @@ -53234,6 +53234,42 @@ var data = "topics": [], "updated_at": 1608129932.0 }, + { + "config_readme": "\u003cp\u003eSimply add your callset under variant-calls, following the structure used in the other already existing callsets.\nMake sure to point to the correct benchmark (CHM-eval, or the two custom WES datasets for the NA12878 GIAB sample that are listed under \u003ccode\u003ecustom-benchmarks\u003c/code\u003e in the config file).\u003c/p\u003e\n", + "data_format": 2, + "description": null, + "formatting": null, + "full_name": "ncbench/ncbench-workflow", + "latest_release": "v1.1.0", + "linting": "InvalidPluginException in file /tmp/tmpdsmdu1yc/ncbench-ncbench-workflow-e64d8c2/workflow/Snakefile, line 45:\nError loading Snakemake plugin http: The package snakemake-storage-plugin-http is not installed.\n", + "mandatory_flags": null, + "report": true, + "software_stack_deployment": { + "conda": true + }, + "standardized": true, + "stargazers_count": 10, + "subscribers_count": 4, + "topics": [], + "updated_at": 1726133128.0 + }, + { + "config_readme": null, + "data_format": 2, + "description": null, + "formatting": "[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\$\u0027\n[DEBUG] In file \"/tmp/tmp6pcg_g2u/rules/classifyReads.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp6pcg_g2u/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp6pcg_g2u/rules/assemble.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmp6pcg_g2u/rules/cleanReads.smk\": NoParametersError: L40: In wildcard_constraints definition.\n[DEBUG] In file \"/tmp/tmp6pcg_g2u/rules/cleanReads.smk\": \n[DEBUG] In file \"/tmp/tmp6pcg_g2u/rules/makeReport.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp6pcg_g2u/rules/annotate.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmp6pcg_g2u/rules/mappingReads.smk\": TabError: inconsistent use of tabs and spaces in indentation (\u003cstring\u003e, line 92)\n[INFO] In file \"/tmp/tmp6pcg_g2u/rules/mappingReads.smk\": 2 file(s) raised parsing errors \ud83e\udd15\n[INFO] In file \"/tmp/tmp6pcg_g2u/rules/mappingReads.smk\": 5 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "healthyPlant/PhytoPipe", + "latest_release": null, + "linting": "Traceback (most recent call last):\n\n File \"/tmp/tmp6pcg_g2u/Snakefile\", line 12, in \u003cmodule\u003e\n CONFIGFILE = str(workflow.overwrite_configfiles[0])\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\nIndexError: list index out of range\n\n\nDuring handling of the above exception, another exception occurred:\n\n\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp6pcg_g2u/Snakefile\", line 14, in \u003cmodule\u003e\n CONFIGFILE = str(workflow.overwrite_configfile[0])\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\nAttributeError: \u0027Workflow\u0027 object has no attribute \u0027overwrite_configfile\u0027. Did you mean: \u0027overwrite_configfiles\u0027?\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 10, + "subscribers_count": 0, + "topics": [], + "updated_at": 1723234279.0 + }, { "config_readme": null, "data_format": 2, @@ -53412,42 +53448,6 @@ var data = ], "updated_at": 1722525200.0 }, - { - "config_readme": "\u003cp\u003eSimply add your callset under variant-calls, following the structure used in the other already existing callsets.\nMake sure to point to the correct benchmark (CHM-eval, or the two custom WES datasets for the NA12878 GIAB sample that are listed under \u003ccode\u003ecustom-benchmarks\u003c/code\u003e in the config file).\u003c/p\u003e\n", - "data_format": 2, - "description": null, - "formatting": null, - "full_name": "ncbench/ncbench-workflow", - "latest_release": "v1.1.0", - "linting": "InvalidPluginException in file /tmp/tmpdsmdu1yc/ncbench-ncbench-workflow-e64d8c2/workflow/Snakefile, line 45:\nError loading Snakemake plugin http: The package snakemake-storage-plugin-http is not installed.\n", - "mandatory_flags": null, - "report": true, - "software_stack_deployment": { - "conda": true - }, - "standardized": true, - "stargazers_count": 10, - "subscribers_count": 4, - "topics": [], - "updated_at": 1726133128.0 - }, - { - "config_readme": null, - "data_format": 2, - "description": null, - "formatting": "[DEBUG] \n\u003cunknown\u003e:1: SyntaxWarning: invalid escape sequence \u0027\\$\u0027\n[DEBUG] In file \"/tmp/tmp6pcg_g2u/rules/classifyReads.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp6pcg_g2u/Snakefile\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp6pcg_g2u/rules/assemble.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmp6pcg_g2u/rules/cleanReads.smk\": NoParametersError: L40: In wildcard_constraints definition.\n[DEBUG] In file \"/tmp/tmp6pcg_g2u/rules/cleanReads.smk\": \n[DEBUG] In file \"/tmp/tmp6pcg_g2u/rules/makeReport.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp6pcg_g2u/rules/annotate.smk\": Formatted content is different from original\n[DEBUG] \n[ERROR] In file \"/tmp/tmp6pcg_g2u/rules/mappingReads.smk\": TabError: inconsistent use of tabs and spaces in indentation (\u003cstring\u003e, line 92)\n[INFO] In file \"/tmp/tmp6pcg_g2u/rules/mappingReads.smk\": 2 file(s) raised parsing errors \ud83e\udd15\n[INFO] In file \"/tmp/tmp6pcg_g2u/rules/mappingReads.smk\": 5 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "healthyPlant/PhytoPipe", - "latest_release": null, - "linting": "Traceback (most recent call last):\n\n File \"/tmp/tmp6pcg_g2u/Snakefile\", line 12, in \u003cmodule\u003e\n CONFIGFILE = str(workflow.overwrite_configfiles[0])\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\nIndexError: list index out of range\n\n\nDuring handling of the above exception, another exception occurred:\n\n\nTraceback (most recent call last):\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/cli.py\", line 2011, in args_to_api\n any_lint = workflow_api.lint()\n ^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 337, in _handle_no_dag\n return method(self, *args, **kwargs)\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/api.py\", line 354, in lint\n workflow.include(\n\n File \"/home/runner/micromamba-root/envs/snakemake-workflow-catalog/lib/python3.12/site-packages/snakemake/workflow.py\", line 1399, in include\n exec(compile(code, snakefile.get_path_or_uri(), \"exec\"), self.globals)\n\n File \"/tmp/tmp6pcg_g2u/Snakefile\", line 14, in \u003cmodule\u003e\n CONFIGFILE = str(workflow.overwrite_configfile[0])\n ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n\nAttributeError: \u0027Workflow\u0027 object has no attribute \u0027overwrite_configfile\u0027. Did you mean: \u0027overwrite_configfiles\u0027?\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 10, - "subscribers_count": 0, - "topics": [], - "updated_at": 1723234279.0 - }, { "config_readme": null, "data_format": 2, @@ -53945,6 +53945,23 @@ var data = "topics": [], "updated_at": 1597229833.0 }, + { + "config_readme": null, + "data_format": 2, + "description": "Analysis code for Olink CVD1 - HF analysis", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpbscm8dmg/alhenry-cvd1-hf-1c98ca6/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "alhenry/cvd1-hf", + "latest_release": "v1.0.0", + "linting": "Lints for rule obs_analysis (line 24, /tmp/tmpbscm8dmg/alhenry-cvd1-hf-1c98ca6/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule MR_analysis (line 50, /tmp/tmpbscm8dmg/alhenry-cvd1-hf-1c98ca6/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule aggregate_MR (line 78, /tmp/tmpbscm8dmg/alhenry-cvd1-hf-1c98ca6/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 12, + "subscribers_count": 2, + "topics": [], + "updated_at": 1723648069.0 + }, { "config_readme": "\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eopen-gira configuration directory\u003c/h1\u003e\u003ca id=\"user-content-open-gira-configuration-directory\" class=\"anchor\" aria-label=\"Permalink: open-gira configuration directory\" href=\"#open-gira-configuration-directory\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eREADME.md\u003c/h2\u003e\u003ca id=\"user-content-readmemd\" class=\"anchor\" aria-label=\"Permalink: README.md\" href=\"#readmemd\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThis file.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003econfig.yaml\u003c/h2\u003e\u003ca id=\"user-content-configyaml\" class=\"anchor\" aria-label=\"Permalink: config.yaml\" href=\"#configyaml\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eYAML configuration file. This file contains parameters that are frequently\nmodified prior to an analysis. Refer to it for more information.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eland_use_to_surface_roughness.csv\u003c/h2\u003e\u003ca id=\"user-content-land_use_to_surface_roughnesscsv\" class=\"anchor\" aria-label=\"Permalink: land_use_to_surface_roughness.csv\" href=\"#land_use_to_surface_roughnesscsv\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eA lookup table from a land use classification scheme to a typical surface\nroughness length. This is used in downscaling wind speeds in tropical-cyclone\nanalyses.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003earc_cluster\u003c/h2\u003e\u003ca id=\"user-content-arc_cluster\" class=\"anchor\" aria-label=\"Permalink: arc_cluster\" href=\"#arc_cluster\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003e\u003ccode\u003esnakemake\u003c/code\u003e profile for running open-gira on the University of Oxford\u0027s ARC\ncluster.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003edamage_curves\u003c/h2\u003e\u003ca id=\"user-content-damage_curves\" class=\"anchor\" aria-label=\"Permalink: damage_curves\" href=\"#damage_curves\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eCSV files, one per \u003ccode\u003easset_type\u003c/code\u003e, describing the relationship between hazard\nintensity and damage fraction. These are used for direct damage estimation.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003ehazard_resource_locations\u003c/h2\u003e\u003ca id=\"user-content-hazard_resource_locations\" class=\"anchor\" aria-label=\"Permalink: hazard_resource_locations\" href=\"#hazard_resource_locations\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eFairly self-explanatory, contains files containing lists of hazard file URLs to\nacquire for analyses.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003eosm_filters\u003c/h2\u003e\u003ca id=\"user-content-osm_filters\" class=\"anchor\" aria-label=\"Permalink: osm_filters\" href=\"#osm_filters\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eText files for use by osmium to \u003ca href=\"https://docs.osmcode.org/osmium/latest/osmium-tags-filter.html\" rel=\"nofollow\"\u003efilter features based on\ntag\u003c/a\u003e. We used\nthese to construct infrastructure networks from OpenStreetMap data.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003erehab_costs\u003c/h2\u003e\u003ca id=\"user-content-rehab_costs\" class=\"anchor\" aria-label=\"Permalink: rehab_costs\" href=\"#rehab_costs\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eCSV files containing rehabilitation cost estimates in USD. One file per sector,\neach row a unique \u003ccode\u003easset_type\u003c/code\u003e.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch2 class=\"heading-element\"\u003estorm_sets\u003c/h2\u003e\u003ca id=\"user-content-storm_sets\" class=\"anchor\" aria-label=\"Permalink: storm_sets\" href=\"#storm_sets\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eJSON files, each containing a single list. The list may contain zero or many\nunique string storm IDs. These can be used to subset a parent \u003ccode\u003eSTORM_SET\u003c/code\u003e, e.g.\nIBTrACS may be subset to contain just storms that hit Mexico since 2000, if the\nrelevant storm IDs are provided. Where the list provided is empty, this is\ninterpreted as \"process every storm in the parent set\", i.e. all of IBTrACS.\u003c/p\u003e\n", "data_format": 2, @@ -53983,23 +54000,6 @@ var data = "topics": [], "updated_at": 1726764841.0 }, - { - "config_readme": null, - "data_format": 2, - "description": "Analysis code for Olink CVD1 - HF analysis", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpbscm8dmg/alhenry-cvd1-hf-1c98ca6/workflow/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "alhenry/cvd1-hf", - "latest_release": "v1.0.0", - "linting": "Lints for rule obs_analysis (line 24, /tmp/tmpbscm8dmg/alhenry-cvd1-hf-1c98ca6/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule MR_analysis (line 50, /tmp/tmpbscm8dmg/alhenry-cvd1-hf-1c98ca6/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n\nLints for rule aggregate_MR (line 78, /tmp/tmpbscm8dmg/alhenry-cvd1-hf-1c98ca6/workflow/Snakefile):\n * No log directive defined:\n Without a log directive, all output will be printed to the terminal. In\n distributed environments, this means that errors are harder to discover.\n In local environments, output of concurrent jobs will be mixed and become\n unreadable.\n Also see:\n https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files\n * Specify a conda environment or container for each rule.:\n This way, the used software for each specific step is documented, and the\n workflow can be executed on any machine without prerequisites.\n Also see:\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management\n https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers\n\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 12, - "subscribers_count": 2, - "topics": [], - "updated_at": 1723648069.0 - }, { "config_readme": null, "data_format": 2, @@ -54166,27 +54166,6 @@ var data = ], "updated_at": 1596079024.0 }, - { - "config_readme": null, - "data_format": 2, - "description": "3DGB is a workflow to build 3D models of genomes from HiC data", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpb1kske06/data-fun-3d-genome-builder-ec5748b/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "data-fun/3d-genome-builder", - "latest_release": "v1.1", - "linting": "KeyError in file /tmp/tmpb1kske06/data-fun-3d-genome-builder-ec5748b/Snakefile, line 3:\n\u0027organism\u0027\n File \"/tmp/tmpb1kske06/data-fun-3d-genome-builder-ec5748b/Snakefile\", line 3, in \u003cmodule\u003e\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 13, - "subscribers_count": 3, - "topics": [ - "hic", - "3d-genome", - "vizualization" - ], - "updated_at": 1726747462.0 - }, { "config_readme": "\u003cp\u003e\u003cem\u003e\u003cstrong\u003ePlease, read carefully.\u003c/strong\u003e\u003c/em\u003e \ud83d\udc0d\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eSetting for memory and threads\u003c/h1\u003e\u003ca id=\"user-content-setting-for-memory-and-threads\" class=\"anchor\" aria-label=\"Permalink: Setting for memory and threads\" href=\"#setting-for-memory-and-threads\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThe rules have been divided in high demanding, medium demanding and low demanding based on testing with different species.\u003c/p\u003e\n\u003cp\u003eIn this part of the \u003ccode\u003econfig.yaml\u003c/code\u003e we can set these values.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003e\ud83c\udf3e 1. Example of suitable values for barley in our testing (genome size ~4.2 Gbp, ~75% of repeats):\u003c/h3\u003e\u003ca id=\"user-content-ear_of_rice-1-example-of-suitable-values-for-barley-in-our-testing-genome-size-42-gbp-75-of-repeats\" class=\"anchor\" aria-label=\"Permalink: :ear_of_rice: 1. Example of suitable values for barley in our testing (genome size ~4.2 Gbp, ~75% of repeats):\" href=\"#ear_of_rice-1-example-of-suitable-values-for-barley-in-our-testing-genome-size-42-gbp-75-of-repeats\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cpre\u003e\u003ccode\u003e# Set memory and threads for high demanding rules\nhigh:\n mem_mb: 409600 # memory in MB\n t: 50 # number of threads\n\n# Set memory and threads for medium demanding rules\nmedium:\n mem_mb: 204800 # memory in MB\n t: 20 # number of threads\n\n# Set memory and threads for low demanding rules\nlow:\n mem_mb: 51200 # memory in MB\n t: 8 # number of threads\n\u003c/code\u003e\u003c/pre\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003e\ud83c\udf44 2. Example of suitable values for R. irregularis in our testing (genome size ~146 Mbp, ~37% of repeats)\u003c/h3\u003e\u003ca id=\"user-content-mushroom-2-example-of-suitable-values-for-r-irregularis-in-our-testing-genome-size-146-mbp-37-of-repeats\" class=\"anchor\" aria-label=\"Permalink: :mushroom: 2. Example of suitable values for R. irregularis in our testing (genome size ~146 Mbp, ~37% of repeats)\" href=\"#mushroom-2-example-of-suitable-values-for-r-irregularis-in-our-testing-genome-size-146-mbp-37-of-repeats\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cpre\u003e\u003ccode\u003e# Set memory and threads for high demanding rules\nhigh:\n mem_mb: 204800 # memory in MB\n t: 50 # number of threads\n\n# Set memory and threads for medium demanding rules\nmedium:\n mem_mb: 20480 # memory in MB\n t: 20 # number of threads\n\n# Set memory and threads for low demanding rules\nlow:\n mem_mb: 10240 # memory in MB\n t: 8 # number of threads\n\u003c/code\u003e\u003c/pre\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003e\ud83c\udf31 2. Example of suitable values for A. thaliana in our testing (genome size ~135 Mbp, ~30% of repeats)\u003c/h3\u003e\u003ca id=\"user-content-seedling-2-example-of-suitable-values-for-a-thaliana-in-our-testing-genome-size-135-mbp-30-of-repeats\" class=\"anchor\" aria-label=\"Permalink: :seedling: 2. Example of suitable values for A. thaliana in our testing (genome size ~135 Mbp, ~30% of repeats)\" href=\"#seedling-2-example-of-suitable-values-for-a-thaliana-in-our-testing-genome-size-135-mbp-30-of-repeats\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cpre\u003e\u003ccode\u003e# Set memory and threads for high demanding rules\nhigh:\n mem_mb: 153600 # memory in MB\n t: 50 # number of threads\n\n# Set memory and threads for medium demanding rules\nmedium:\n mem_mb: 20480 # memory in MB\n t: 20 # number of threads\n\n# Set memory and threads for low demanding rules\nlow:\n mem_mb: 10240 # memory in MB\n t: 8 # number of threads\n\u003c/code\u003e\u003c/pre\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003e\ud83c\udf4e 2. Example of suitable values for apple in our testing (genome size ~700 Mbp, ~51% of repeats)\u003c/h3\u003e\u003ca id=\"user-content-apple-2-example-of-suitable-values-for-apple-in-our-testing-genome-size-700-mbp-51-of-repeats\" class=\"anchor\" aria-label=\"Permalink: :apple: 2. Example of suitable values for apple in our testing (genome size ~700 Mbp, ~51% of repeats)\" href=\"#apple-2-example-of-suitable-values-for-apple-in-our-testing-genome-size-700-mbp-51-of-repeats\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cpre\u003e\u003ccode\u003e# Set memory and threads for high demanding rules\nhigh:\n mem_mb: 307200 # memory in MB\n t: 50 # number of threads\n\n# Set memory and threads for medium demanding rules\nmedium:\n mem_mb: 20480 # memory in MB\n t: 20 # number of threads\n\n# Set memory and threads for low demanding rules\nlow:\n mem_mb: 10240 # memory in MB\n t: 8 # number of threads\n\u003c/code\u003e\u003c/pre\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003ePaths to reads\u003c/h1\u003e\u003ca id=\"user-content-paths-to-reads\" class=\"anchor\" aria-label=\"Permalink: Paths to reads\" href=\"#paths-to-reads\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eBelow is an example of how to set the paths to hifi and hic reads. It\u0027s showing the case in which hifi and hic have been placed under \u003ccode\u003eresources/raw_hifi\u003c/code\u003e and \u003ccode\u003eresources/raw_hic\u003c/code\u003e directories into \u003ccode\u003ecolora\u003c/code\u003e directory itself, respectively. It\u0027s also possible to specify different paths if you prefer, but please notice that if you are not using subdirectories of \u003ccode\u003ecolora\u003c/code\u003e itself you should use absolute paths.\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003e# Path to hifi reads\nhifi_path: \"resources/raw_hifi/\"\n\n# Path to hic reads\nhic_path: \"resources/raw_hic/\"\n\u003c/code\u003e\u003c/pre\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eKMC and genomescope2\u003c/h1\u003e\u003ca id=\"user-content-kmc-and-genomescope2\" class=\"anchor\" aria-label=\"Permalink: KMC and genomescope2\" href=\"#kmc-and-genomescope2\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eKMC produces the k-mer database that is then used by genomescope2 to have an estimate of the genome sie and other statistics. Therefore, parameters set for KMC are going to influence the behaviour of genomescope2 as well.\u003c/p\u003e\n\u003cp\u003eThe k-mer size, if unsure, can be estimated using a script provided by Merqury, called \u003ccode\u003ebest_k.sh\u003c/code\u003e, available \u003ca href=\"https://github.com/marbl/merqury/blob/master/best_k.sh\"\u003ehere\u003c/a\u003e.\u003c/p\u003e\n\u003cp\u003eFor the parameter \u003ccode\u003ecs\u003c/code\u003e you must pay attention to your genome size and repetitiveness, as this can lead to wrong estimation of genome size. See \u003ca href=\"https://github.com/tbenavi1/genomescope2.0?tab=readme-ov-file#frequently-asked-questions-faq\"\u003egenomescope2 FAQs\u003c/a\u003e.\u003c/p\u003e\n\u003cp\u003eThe parameter \u003ccode\u003e-p\u003c/code\u003e for genomescope sets the ploidy of the model for GenomeScope to use. See \u003ca href=\"https://github.com/tbenavi1/genomescope2.0\"\u003egenomescope2 repo\u003c/a\u003e for further details.\u003c/p\u003e\n\u003cp\u003eThe parameter \u003ccode\u003e-l\u003c/code\u003e for genomescope sets the estimated coverage of the 1n peak. See \u003ca href=\"https://github.com/tbenavi1/genomescope2.0\"\u003egenomescope2 repo\u003c/a\u003e for further details.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003e\ud83c\udf3e 1. Example of suitable parameters for barley in our testing (genome size ~4.2 Gbp, 75% of repeats):\u003c/h3\u003e\u003ca id=\"user-content-ear_of_rice-1-example-of-suitable-parameters-for-barley-in-our-testing-genome-size-42-gbp-75-of-repeats\" class=\"anchor\" aria-label=\"Permalink: :ear_of_rice: 1. Example of suitable parameters for barley in our testing (genome size ~4.2 Gbp, 75% of repeats):\" href=\"#ear_of_rice-1-example-of-suitable-parameters-for-barley-in-our-testing-genome-size-42-gbp-75-of-repeats\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cpre\u003e\u003ccode\u003e# Customisable parameters for kmc\nkmc:\n k: 21 # kmer size, it will be the same used for genomescope2\n ci: 1 # exclude k-mers occurring less than \u0026lt;value\u0026gt; times (default: 2)\n cs: 1000000 #maximal value of a counter (default: 255)\n\n# Customisable parameters for kmc_tools transform\nkmc_tools:\n cx: 1000000 # exclude k-mers occurring more of than \u0026lt;value\u0026gt; times\n\n# Customisable parameters for genomescope2\ngenomescope2:\n optional_params:\n \"-p\": \"1\"\n \"-l\": \"\"\n\u003c/code\u003e\u003c/pre\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eoatk\u003c/h1\u003e\u003ca id=\"user-content-oatk\" class=\"anchor\" aria-label=\"Permalink: oatk\" href=\"#oatk\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eSee usage section for instructions on how to obtain the oatk database of interest.\u003c/p\u003e\n\u003cp\u003eNote that the \u003ccode\u003ec\u003c/code\u003e parameter, which specifies coverage threshold, can be set as 5-10 times the value of nuclear sequence coverage.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003e\ud83c\udf3e 1. Example of suitable parameters for barley in our testing (hifi coverage ~30x):\u003c/h3\u003e\u003ca id=\"user-content-ear_of_rice-1-example-of-suitable-parameters-for-barley-in-our-testing-hifi-coverage-30x\" class=\"anchor\" aria-label=\"Permalink: :ear_of_rice: 1. Example of suitable parameters for barley in our testing (hifi coverage ~30x):\" href=\"#ear_of_rice-1-example-of-suitable-parameters-for-barley-in-our-testing-hifi-coverage-30x\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cpre\u003e\u003ccode\u003e# Customisable parameters for oatk\noatk:\n k: 1001 # kmer size [1001]\n c: 150 # minimum kmer coverage [3]\n m: \"resources/oatkDB/embryophyta_mito.fam\" # mitochondria gene annotation HMM profile database [NULL]\n optional_params: \n \"-p\": \"resources/oatkDB/embryophyta_pltd.fam\" # to use for species that have a plastid db\n\u003c/code\u003e\u003c/pre\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003efastp\u003c/h1\u003e\u003ca id=\"user-content-fastp\" class=\"anchor\" aria-label=\"Permalink: fastp\" href=\"#fastp\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eFastp is used for the preprocessing of the hic reads. Adapters are always removed, while it is suggested to use the optional parameters in the \u003ccode\u003econfig.yaml\u003c/code\u003e when the data are obtained with Arima Hi-C library prep kit.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003e1. Example of parameters to be used with data obtained with Arima Hi-C library prep kit:\u003c/h3\u003e\u003ca id=\"user-content-1-example-of-parameters-to-be-used-with-data-obtained-with-arima-hi-c-library-prep-kit\" class=\"anchor\" aria-label=\"Permalink: 1. Example of parameters to be used with data obtained with Arima Hi-C library prep kit:\" href=\"#1-example-of-parameters-to-be-used-with-data-obtained-with-arima-hi-c-library-prep-kit\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cpre\u003e\u003ccode\u003e# Customisable parameters for fastp\nfastp:\n optional_params:\n \"--cut_front\": True # to use only with Arima Hi-C library prep kit generated data\n \"--cut_front_window_size\": \"5\" # to use only with Arima Hi-C library prep kit generated data\n\u003c/code\u003e\u003c/pre\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003e2. Example of parameters to be used with other library prep kit:\u003c/h3\u003e\u003ca id=\"user-content-2-example-of-parameters-to-be-used-with-other-library-prep-kit\" class=\"anchor\" aria-label=\"Permalink: 2. Example of parameters to be used with other library prep kit:\" href=\"#2-example-of-parameters-to-be-used-with-other-library-prep-kit\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cpre\u003e\u003ccode\u003e# Customisable parameters for fastp\nfastp:\n optional_params:\n \"--cut_front\": False # to use only with Arima Hi-C library prep kit generated data\n \"--cut_front_window_size\": \"\" # to use only with Arima Hi-C library prep kit generated data\n\u003c/code\u003e\u003c/pre\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003ehifiasm\u003c/h1\u003e\u003ca id=\"user-content-hifiasm\" class=\"anchor\" aria-label=\"Permalink: hifiasm\" href=\"#hifiasm\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eHifiasm is the assembler used by colora. It is possible to obtain a primary assembly or a phased assembly with colora. You can choose this by setting \u003ccode\u003ephased_assembly: False\u003c/code\u003e or \u003ccode\u003ephased_assembly: True\u003c/code\u003e respectively in the \u003ccode\u003econfig.yaml\u003c/code\u003e. In the case of phased assembly, Hi-C reads are integrated in the assembly process, after being pre-processed with fastp to remove adapters (and 5\u0027 ends in the case of Arima library prep kit).\u003c/p\u003e\n\u003cp\u003eAll the other parameters are optional, and you can refer to \u003ca href=\"https://hifiasm.readthedocs.io/en/latest/index.html\" rel=\"nofollow\"\u003ehifiasm documentation\u003c/a\u003e to understand what is optimal for your case.\u003c/p\u003e\n\u003cp\u003eIf you also have ONT reads for your sample, you may consider using them in the assembly process. Remember that you should previously trim them (if needed) and join them in a single file (if they are in multiple files).\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003e1. Example of primary assembly (hifiasm uses only HiFi reads in this case):\u003c/h3\u003e\u003ca id=\"user-content-1-example-of-primary-assembly-hifiasm-uses-only-hifi-reads-in-this-case\" class=\"anchor\" aria-label=\"Permalink: 1. Example of primary assembly (hifiasm uses only HiFi reads in this case):\" href=\"#1-example-of-primary-assembly-hifiasm-uses-only-hifi-reads-in-this-case\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cpre\u003e\u003ccode\u003e# Customisable parameters for hifiasm\nhifiasm:\n phased_assembly: False # set to true if you want to obtain a phased assembly\n optional_params:\n \"-f\": \"\" # used for small datasets\n \"-l\": \"\" # purge level. 0: no purging; 1: light; 2/3: aggressive [0 for trio; 3 for unzip]\n \"--ul\": \"\" # use this if you have also ont data yu want to integrate in your assembly\n\u003c/code\u003e\u003c/pre\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003e2. Example of primary assembly using HiFi and ONT reads:\u003c/h3\u003e\u003ca id=\"user-content-2-example-of-primary-assembly-using-hifi-and-ont-reads\" class=\"anchor\" aria-label=\"Permalink: 2. Example of primary assembly using HiFi and ONT reads:\" href=\"#2-example-of-primary-assembly-using-hifi-and-ont-reads\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cpre\u003e\u003ccode\u003e# Customisable parameters for hifiasm\nhifiasm:\n phased_assembly: False # set to true if you want to obtain a phased assembly\n optional_params:\n \"-f\": \"\" # used for small datasets\n \"-l\": \"\" # purge level. 0: no purging; 1: light; 2/3: aggressive [0 for trio; 3 for unzip]\n \"--ul\": \"resources/raw_ont/ont_reads.fastq.gz\" # use this if you have also ont data you want to integrate in your assembly\n\u003c/code\u003e\u003c/pre\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003e3. Example of phased assembly with extra optional parameters (in this case HiFi and Hi-C reads are used):\u003c/h3\u003e\u003ca id=\"user-content-3-example-of-phased-assembly-with-extra-optional-parameters-in-this-case-hifi-and-hi-c-reads-are-used\" class=\"anchor\" aria-label=\"Permalink: 3. Example of phased assembly with extra optional parameters (in this case HiFi and Hi-C reads are used):\" href=\"#3-example-of-phased-assembly-with-extra-optional-parameters-in-this-case-hifi-and-hi-c-reads-are-used\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cpre\u003e\u003ccode\u003e# Customisable parameters for hifiasm\nhifiasm:\n phased_assembly: True # set to true if you want to obtain a phased assembly\n optional_params:\n \"--hom-cov\": \"181\"\n \"-f\": \"\" # used for small datasets\n \"-l\": \"\" # purge level. 0: no purging; 1: light; 2/3: aggressive [0 for trio; 3 for unzip]\n \"--ul\": \"\" # use this if you have also ont data yu want to integrate in your assembly\n\u003c/code\u003e\u003c/pre\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003e4. Example of phased assembly with ONT integration (in this case HiFi, Hi-C and ONT reads are used):\u003c/h3\u003e\u003ca id=\"user-content-4-example-of-phased-assembly-with-ont-integration-in-this-case-hifi-hi-c-and-ont-reads-are-used\" class=\"anchor\" aria-label=\"Permalink: 4. Example of phased assembly with ONT integration (in this case HiFi, Hi-C and ONT reads are used):\" href=\"#4-example-of-phased-assembly-with-ont-integration-in-this-case-hifi-hi-c-and-ont-reads-are-used\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cpre\u003e\u003ccode\u003e# Customisable parameters for hifiasm\nhifiasm:\n phased_assembly: True # set to true if you want to obtain a phased assembly\n optional_params:\n \"-f\": \"\" # used for small datasets\n \"-l\": \"\" # purge level. 0: no purging; 1: light; 2/3: aggressive [0 for trio; 3 for unzip]\n \"--ul\": \"resources/raw_ont/ont_reads.fastq.gz\" # use this if you have also ont data yu want to integrate in your assembly\n\u003c/code\u003e\u003c/pre\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eFCS-gx\u003c/h1\u003e\u003ca id=\"user-content-fcs-gx\" class=\"anchor\" aria-label=\"Permalink: FCS-gx\" href=\"#fcs-gx\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eFCS-gx is the tool that performs the decontamination of the assembly. However, this rule can be skipped setting \u003ccode\u003einclude_fcsgx: False\u003c/code\u003e. This choice is made given the fact that the database that FCS-gx uses is ~500GB, and it needs a big RAM, and we want colora to be as portable as possible. Skipping this rule it\u0027s possible to run colora even in a small system.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003e\ud83c\udf3e 1. Example of suitable parameters for barley:\u003c/h3\u003e\u003ca id=\"user-content-ear_of_rice-1-example-of-suitable-parameters-for-barley\" class=\"anchor\" aria-label=\"Permalink: :ear_of_rice: 1. Example of suitable parameters for barley:\" href=\"#ear_of_rice-1-example-of-suitable-parameters-for-barley\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cpre\u003e\u003ccode\u003e#Set this to False if you want to skip the fcsgx step:\ninclude_fcsgx: True #inlcude this rule only if you have preiously downloaded the database (recommended to run fcsgx only on a HPC. It requires around 500 GB of space on your disk and a large RAM)\n\n# Customisable parameters for fcsgx\nfcsgx:\n ncbi_tax_id: 4513\n path_to_gx_db: \"resources/gxdb\"\n\u003c/code\u003e\u003c/pre\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003e\ud83c\udf44 2. Example of suitable parameters for Rhizophagus irregularis:\u003c/h3\u003e\u003ca id=\"user-content-mushroom-2-example-of-suitable-parameters-for-rhizophagus-irregularis\" class=\"anchor\" aria-label=\"Permalink: :mushroom: 2. Example of suitable parameters for Rhizophagus irregularis:\" href=\"#mushroom-2-example-of-suitable-parameters-for-rhizophagus-irregularis\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cpre\u003e\u003ccode\u003e#Set this to False if you want to skip the fcsgx step:\ninclude_fcsgx: True #inlcude this rule only if you have preiously downloaded the database (recommended to run fcsgx only on a HPC. It requires around 500 GB of space on your disk and a large RAM)\n\n# Customisable parameters for fcsgx\nfcsgx:\n ncbi_tax_id: 588596\n path_to_gx_db: \"resources/gxdb\"\n\u003c/code\u003e\u003c/pre\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003epurge_dups\u003c/h1\u003e\u003ca id=\"user-content-purge_dups\" class=\"anchor\" aria-label=\"Permalink: purge_dups\" href=\"#purge_dups\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003ePurge_dups is a tool used in most of the assembly pipelines to purge haplotigs and overlaps in an assembly based on read depth. In \u003ccode\u003ecolora\u003c/code\u003e, the rule used to run this tool is run only when \u003ccode\u003ephased_assembly: False\u003c/code\u003e is set for hifiasm, it is optional and can be skipped setting \u003ccode\u003einclude_purge_dups: False\u003c/code\u003e. This is because in some of our projects we found that purge_dups was excluding biological relevant information from the assembly, giving worse busco scores compared to the assembly obtained skipping this rule. However, it may be beneficial to try several settings (including purge_dups or not) to see what combinations is the best for your case.\u003c/p\u003e\n\u003cp\u003eWhen \u003ccode\u003ephased_assembly: True\u003c/code\u003e is set for hifiasm, it is mandatory to set \u003ccode\u003einclude_purge_dups: False\u003c/code\u003e. This is because the purging step is not necessary when we obtain two assembly for two different haplotypes.\u003c/p\u003e\n\u003cp\u003eWhen \u003ccode\u003ephased_assembly: False\u003c/code\u003e is set for hifiasm, you can choose to set \u003ccode\u003einclude_purge_dups: True\u003c/code\u003e or \u003ccode\u003einclude_purge_dups: False\u003c/code\u003e. Again, we recommend to try both ways to see what strategy gives better results.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eArima genomics mapping pipeline\u003c/h1\u003e\u003ca id=\"user-content-arima-genomics-mapping-pipeline\" class=\"anchor\" aria-label=\"Permalink: Arima genomics mapping pipeline\" href=\"#arima-genomics-mapping-pipeline\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eThis pipeline has been integrated in colora, translating it from the \u003ca href=\"https://github.com/ArimaGenomics/mapping_pipeline\"\u003eoriginal bash pipeline\u003c/a\u003e to a snakemake version.\u003c/p\u003e\n\u003cp\u003eThe only changes we made compared to the original pipeline are the following:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003eRemove the PREFIX line and the option -p $PREFIX from the bwa command (step 0 of the original pipeline)\u003c/li\u003e\n\u003cli\u003eadd -M flag in bwa mem command (step 1.A and 1.B of the original pipeline)\u003c/li\u003e\n\u003cli\u003epipeline split in several rules\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eMoreover, colora doesn\u0027t handle technical and biological replicates of Hi-C reads, so you must refer to the original pipeline for that.\u003c/p\u003e\n\u003cp\u003eThe preprocessing of the Hi-C reads is made with fastp (see above).\u003c/p\u003e\n\u003cp\u003eSamples can be processed only one by one with this pipeline.\u003c/p\u003e\n\u003cp\u003eIf you set \u003ccode\u003ephased_assembly: True\u003c/code\u003e for hifiasm, the two assemblies for the different haplotypes are processed in parallel.\u003c/p\u003e\n\u003cp\u003eThe only parameter you can custumise for the arima genomics mapping pipeline is the mapping quality filter (10 is the default):\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003e1. Example of default mapping quality filter for arima mapping pipeline\u003c/h3\u003e\u003ca id=\"user-content-1-example-of-default-mapping-quality-filter-for-arima-mapping-pipeline\" class=\"anchor\" aria-label=\"Permalink: 1. Example of default mapping quality filter for arima mapping pipeline\" href=\"#1-example-of-default-mapping-quality-filter-for-arima-mapping-pipeline\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cpre\u003e\u003ccode\u003e# Customisable parameters for arima mapping pipeline:\narima:\n MAPQ_FILTER: 10\n\u003c/code\u003e\u003c/pre\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eyahs\u003c/h1\u003e\u003ca id=\"user-content-yahs\" class=\"anchor\" aria-label=\"Permalink: yahs\" href=\"#yahs\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eYaHS is the tool that we use for performing the scaffolding on the contig level assembly using Hi-C reads.\u003c/p\u003e\n\u003cp\u003eThe only customisable parameter for yahs in \u003ccode\u003ecolora\u003c/code\u003e is the restriction enzyme(s), but it is an optional parameter and you can choose to set it or not:\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003e# Customisable parameters for yahs\nyahs:\n optional_params: \n \"-e\": \"\" # you can specify the restriction enzyme(s) used by the Hi-C experiment\n\u003c/code\u003e\u003c/pre\u003e\n\u003cp\u003eN.B. From \u003ca href=\"https://github.com/c-zhou/yahs\"\u003eYaHS documentation\u003c/a\u003e:\u003c/p\u003e\n\u003cblockquote\u003e\n\u003cp\u003eWith -e option, you can specify the restriction enzyme(s) used by the Hi-C experiment. For example, GATC for the DpnII restriction enzyme used by the Dovetail Hi-C Kit; GATC,GANTC and GATC,GANTC,CTNAG,TTAA for Arima genomics 2-enzyme and 4-enzyme protocol, respectively. Sometimes, the specification of enzymes may not change the scaffolding result very much if not make it worse, especially when the base quality of the assembly is not very good, e.g., assembies constructed from noisy long reads.\u003c/p\u003e\n\u003c/blockquote\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eQuast\u003c/h1\u003e\u003ca id=\"user-content-quast\" class=\"anchor\" aria-label=\"Permalink: Quast\" href=\"#quast\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eQuast is used to perform the quality check of the assembly along all the workflow. It processes:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003econtig level assembly(ies) produced by hifiasm\u003c/li\u003e\n\u003cli\u003edecontaminated contig level assembly(ies) produced by fcs-gx (if included)\u003c/li\u003e\n\u003cli\u003epurged contig level primary assembly produced by purge_dups (if included)\u003c/li\u003e\n\u003cli\u003escaffolded assembly(ies) produced by yahs\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eYou can optionally give as input the reference genome for the species under study to compare you assembly with.\u003c/p\u003e\n\u003cp\u003eAll the parameters that you can customise for quast are optional, and you can refer to \u003ca href=\"https://quast.sourceforge.net/docs/manual.html\" rel=\"nofollow\"\u003equast documentation\u003c/a\u003e to see which ones are suitable for your case.\u003c/p\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003e1. Example running quast with no reference genome\u003c/h3\u003e\u003ca id=\"user-content-1-example-running-quast-with-no-reference-genome\" class=\"anchor\" aria-label=\"Permalink: 1. Example running quast with no reference genome\" href=\"#1-example-running-quast-with-no-reference-genome\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eIn this case just leave all the optional parameters empty:\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003e# Customisable parameters for quast\nquast:\n optional_params: \n \"--fragmented\": \"\"\n \"--large\": \"\"\n\u003c/code\u003e\u003c/pre\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch3 class=\"heading-element\"\u003e2. Example running quast with reference genome\u003c/h3\u003e\u003ca id=\"user-content-2-example-running-quast-with-reference-genome\" class=\"anchor\" aria-label=\"Permalink: 2. Example running quast with reference genome\" href=\"#2-example-running-quast-with-reference-genome\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eIn this case you have to previously download your reference genome (and GFF, if you want), and specify the path with the \u003ccode\u003e-r\u003c/code\u003e flag (\u003ccode\u003e-g\u003c/code\u003e for the GFF):\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003e# Customisable parameters for quast\nquast:\n optional_params: \n \"--fragmented\": \"\"\n \"--large\": \"\"\n \"-r\": \"resources/reference_genomes/yeast/Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa\"\n \"-g\": \"resources/reference_genomes/yeast/Saccharomyces_cerevisiae.R64-1-1.101.gff3\"\n\u003c/code\u003e\u003c/pre\u003e\n\u003cdiv class=\"markdown-heading\"\u003e\u003ch1 class=\"heading-element\"\u003eBusco\u003c/h1\u003e\u003ca id=\"user-content-busco\" class=\"anchor\" aria-label=\"Permalink: Busco\" href=\"#busco\"\u003e\u003cspan aria-hidden=\"true\" class=\"octicon octicon-link\"\u003e\u003c/span\u003e\u003c/a\u003e\u003c/div\u003e\n\u003cp\u003eBusco is used to perform the quality check of the assembly along all the workflow. It processes:\u003c/p\u003e\n\u003cul\u003e\n\u003cli\u003econtig level assembly(ies) produced by hifiasm\u003c/li\u003e\n\u003cli\u003edecontaminated contig level assembly(ies) produced by fcs-gx (if included)\u003c/li\u003e\n\u003cli\u003epurged contig level primary assembly produced by purge_dups (if included)\u003c/li\u003e\n\u003cli\u003escaffolded assembly(ies) produced by yahs\u003c/li\u003e\n\u003c/ul\u003e\n\u003cp\u003eYou must download the busco lineage of your interest before running colora. See \u003ca href=\"https://github.com/LiaOb21/colora/tree/main?tab=readme-ov-file#snakemake-workflow-colora\"\u003ehere\u003c/a\u003e for instructions on how to download the busco lineage.\u003c/p\u003e\n\u003cp\u003eYou need to specify the path to your busco lineage in the config file. Additionally, you can set further optional parameters. For example, if you prefer to use metaeuk rathern than miniprot (which is the default for busco), you can customise the \u003ccode\u003econfig.yaml\u003c/code\u003e as follows:\u003c/p\u003e\n\u003cpre\u003e\u003ccode\u003e# Customisable parameters for busco\nbusco:\n lineage: \"resources/saccharomycetes_odb10\" # lineage to be used for busco analysis\n optional_params: \n \"--metaeuk\": True\n\u003c/code\u003e\u003c/pre\u003e\n\u003cp\u003eIf you want the default parameters (minprot), you can set \u003ccode\u003e\"--metaeuk\": \"\"\u003c/code\u003e.\u003c/p\u003e\n", "data_format": 2, @@ -54216,6 +54195,27 @@ var data = ], "updated_at": 1726676255.0 }, + { + "config_readme": null, + "data_format": 2, + "description": "3DGB is a workflow to build 3D models of genomes from HiC data", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmpb1kske06/data-fun-3d-genome-builder-ec5748b/Snakefile\": Formatted content is different from original\n[INFO] 1 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "data-fun/3d-genome-builder", + "latest_release": "v1.1", + "linting": "KeyError in file /tmp/tmpb1kske06/data-fun-3d-genome-builder-ec5748b/Snakefile, line 3:\n\u0027organism\u0027\n File \"/tmp/tmpb1kske06/data-fun-3d-genome-builder-ec5748b/Snakefile\", line 3, in \u003cmodule\u003e\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 13, + "subscribers_count": 3, + "topics": [ + "hic", + "3d-genome", + "vizualization" + ], + "updated_at": 1726747462.0 + }, { "config_readme": null, "data_format": 2, @@ -55537,23 +55537,6 @@ var data = ], "updated_at": 1718131532.0 }, - { - "config_readme": null, - "data_format": 2, - "description": "A workflow and scripts for large-scale antiSMASH analyses", - "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp3vjbco8l/zreitz-multismash-71ddf42/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp3vjbco8l/zreitz-multismash-71ddf42/workflow/Snakefile\": Formatted content is different from original\n[INFO] 2 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", - "full_name": "zreitz/multismash", - "latest_release": "v0.4.0", - "linting": "IndexError in file /tmp/tmp3vjbco8l/zreitz-multismash-71ddf42/workflow/rules/common.smk, line 8:\nlist index out of range\n File \"/tmp/tmp3vjbco8l/zreitz-multismash-71ddf42/workflow/Snakefile\", line 5, in \u003cmodule\u003e\n File \"/tmp/tmp3vjbco8l/zreitz-multismash-71ddf42/workflow/rules/common.smk\", line 8, in build_paths\n", - "mandatory_flags": [], - "report": false, - "software_stack_deployment": null, - "standardized": false, - "stargazers_count": 27, - "subscribers_count": 2, - "topics": [], - "updated_at": 1726979356.0 - }, { "config_readme": null, "data_format": 2, @@ -55577,6 +55560,23 @@ var data = ], "updated_at": 1723034334.0 }, + { + "config_readme": null, + "data_format": 2, + "description": "A workflow and scripts for large-scale antiSMASH analyses", + "formatting": "[DEBUG] \n[DEBUG] In file \"/tmp/tmp3vjbco8l/zreitz-multismash-71ddf42/workflow/rules/common.smk\": Formatted content is different from original\n[DEBUG] \n[DEBUG] In file \"/tmp/tmp3vjbco8l/zreitz-multismash-71ddf42/workflow/Snakefile\": Formatted content is different from original\n[INFO] 2 file(s) would be changed \ud83d\ude2c\n\nsnakefmt version: 0.10.2", + "full_name": "zreitz/multismash", + "latest_release": "v0.4.0", + "linting": "IndexError in file /tmp/tmp3vjbco8l/zreitz-multismash-71ddf42/workflow/rules/common.smk, line 8:\nlist index out of range\n File \"/tmp/tmp3vjbco8l/zreitz-multismash-71ddf42/workflow/Snakefile\", line 5, in \u003cmodule\u003e\n File \"/tmp/tmp3vjbco8l/zreitz-multismash-71ddf42/workflow/rules/common.smk\", line 8, in build_paths\n", + "mandatory_flags": [], + "report": false, + "software_stack_deployment": null, + "standardized": false, + "stargazers_count": 27, + "subscribers_count": 2, + "topics": [], + "updated_at": 1726979356.0 + }, { "config_readme": null, "data_format": 2, diff --git a/skips.json b/skips.json index 89a9698..f25a4b6 100644 --- a/skips.json +++ b/skips.json @@ -1,4 +1,184 @@ [ + { + "full_name": "Immunodynamics-Engel-Lab/msiflow", + "updated_at": 1726522910.0 + }, + { + "full_name": "ETH-NEXUS/scAmpi_single_cell_RNA", + "updated_at": 1723796701.0 + }, + { + "full_name": "vpandey-om/MCAgeneKO", + "updated_at": 1723712097.0 + }, + { + "full_name": "bfairkun/cookiecutter-wflowR-smk", + "updated_at": 1723664497.0 + }, + { + "full_name": "dib-lab/portable-snakemake-workflows", + "updated_at": 1723659316.0 + }, + { + "full_name": "ammattita6i/awesome-pipeline", + "updated_at": 1723648653.0 + }, + { + "full_name": "KTH-dESA/OSeMBE_ECEMF", + "updated_at": 1725458074.0 + }, + { + "full_name": "snakemake/poetry-snakemake-plugin", + "updated_at": 1723646665.0 + }, + { + "full_name": "gagneurlab/drop", + 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