diff --git a/workflows/variant-calling/haploid-variant-calling-wgs-pe/CHANGELOG.md b/workflows/variant-calling/haploid-variant-calling-wgs-pe/CHANGELOG.md index fda7e77e6..7720b1803 100644 --- a/workflows/variant-calling/haploid-variant-calling-wgs-pe/CHANGELOG.md +++ b/workflows/variant-calling/haploid-variant-calling-wgs-pe/CHANGELOG.md @@ -1,5 +1,17 @@ # Changelog +## [0.2] 2024-11-18 + +### Automatic update +- `toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.24.0+galaxy3` +- `toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/4.3+T.galaxy6` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff_build_gb/5.2+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18` +- `toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.13+galaxy1` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.20+galaxy3` +- `toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.2+galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/samtools_stats/samtools_stats/2.0.5` +- `toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.2` was updated to `toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0` +- `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0` +- `toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2` was updated to `toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/5.2+galaxy0` + ## [0.1] diff --git a/workflows/variant-calling/haploid-variant-calling-wgs-pe/WGS-PE-variant-calling-in-haploid-system.ga b/workflows/variant-calling/haploid-variant-calling-wgs-pe/WGS-PE-variant-calling-in-haploid-system.ga index 97786122c..89b4af576 100644 --- a/workflows/variant-calling/haploid-variant-calling-wgs-pe/WGS-PE-variant-calling-in-haploid-system.ga +++ b/workflows/variant-calling/haploid-variant-calling-wgs-pe/WGS-PE-variant-calling-in-haploid-system.ga @@ -12,7 +12,7 @@ "format-version": "0.1", "license": "MIT", "name": "Paired end variant calling in haploid system", - "release": "0.1", + "release": "0.2", "report": { "markdown": "\n# Workflow Execution Report\n\n## Workflow Inputs\n```galaxy\ninvocation_inputs()\n```\n\n## Workflow Outputs\n```galaxy\ninvocation_outputs()\n```\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n" }, @@ -100,7 +100,7 @@ }, "3": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.24.0+galaxy3", "errors": null, "id": 3, "input_connections": { @@ -142,15 +142,15 @@ "output_name": "report_json" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.24.0+galaxy3", "tool_shed_repository": { - "changeset_revision": "65b93b623c77", + "changeset_revision": "a626e8c0e1ba", "name": "fastp", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"filter_options\": {\"quality_filtering_options\": {\"disable_quality_filtering\": false, \"qualified_quality_phred\": null, \"unqualified_percent_limit\": null, \"n_base_limit\": null}, \"length_filtering_options\": {\"disable_length_filtering\": false, \"length_required\": null, \"length_limit\": null}, \"low_complexity_filter\": {\"enable_low_complexity_filter\": false, \"complexity_threshold\": null}}, \"output_options\": {\"report_html\": true, \"report_json\": true}, \"overrepresented_sequence_analysis\": {\"overrepresentation_analysis\": false, \"overrepresentation_sampling\": null}, \"read_mod_options\": {\"polyg_tail_trimming\": {\"trimming_select\": \"\", \"__current_case__\": 1, \"poly_g_min_len\": null}, \"polyx_tail_trimming\": {\"polyx_trimming_select\": \"\", \"__current_case__\": 1}, \"umi_processing\": {\"umi\": false, \"umi_loc\": \"\", \"umi_len\": null, \"umi_prefix\": \"\"}, \"cutting_by_quality_options\": {\"cut_by_quality5\": false, \"cut_by_quality3\": false, \"cut_window_size\": null, \"cut_mean_quality\": null}, \"base_correction_options\": {\"correction\": false}}, \"single_paired\": {\"single_paired_selector\": \"paired_collection\", \"__current_case__\": 2, \"paired_input\": {\"__class__\": \"ConnectedValue\"}, \"adapter_trimming_options\": {\"disable_adapter_trimming\": false, \"adapter_sequence1\": \"\", \"adapter_sequence2\": \"\"}, \"global_trimming_options\": {\"trim_front1\": null, \"trim_tail1\": null, \"trim_front2\": null, \"trim_tail2\": null}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "0.23.2+galaxy0", + "tool_state": "{\"filter_options\": {\"quality_filtering_options\": {\"disable_quality_filtering\": false, \"qualified_quality_phred\": null, \"unqualified_percent_limit\": null, \"n_base_limit\": null}, \"length_filtering_options\": {\"disable_length_filtering\": false, \"length_required\": null, \"length_limit\": null}, \"low_complexity_filter\": {\"enable_low_complexity_filter\": false, \"complexity_threshold\": null}}, \"output_options\": {\"report_html\": true, \"report_json\": true}, \"overrepresented_sequence_analysis\": {\"overrepresentation_analysis\": false, \"overrepresentation_sampling\": null}, \"read_mod_options\": {\"polyg_tail_trimming\": {\"trimming_select\": \"\", \"__current_case__\": 1, \"poly_g_min_len\": null}, \"polyx_tail_trimming\": {\"polyx_trimming_select\": \"\", \"__current_case__\": 1}, \"umi_processing\": {\"umi\": false, \"umi_loc\": \"\", \"umi_len\": null, \"umi_prefix\": \"\"}, \"cutting_by_quality_options\": {\"cut_by_quality5\": false, \"cut_by_quality3\": false, \"cut_window_size\": null, \"cut_mean_quality\": null}, \"base_correction_options\": {\"correction\": false}}, \"single_paired\": {\"single_paired_selector\": \"paired_collection\", \"__current_case__\": 2, \"paired_input\": {\"__class__\": \"ConnectedValue\"}, \"merge_reads\": {\"merge\": \"\", \"__current_case__\": 1}, \"adapter_trimming_options\": {\"disable_adapter_trimming\": false, \"adapter_sequence1\": \"\", \"adapter_sequence2\": \"\", \"detect_adapter_for_pe\": false}, \"global_trimming_options\": {\"trim_front1\": null, \"trim_tail1\": null, \"trim_front2\": null, \"trim_tail2\": null}}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "0.24.0+galaxy3", "type": "tool", "uuid": "aab66ae3-1955-46f0-b0b8-9d6374b81d8a", "when": null, @@ -164,7 +164,7 @@ }, "4": { "annotation": "", - 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"tool_version": "4.3+T.galaxy6", + "tool_version": "5.2+galaxy0", "type": "tool", "uuid": "691404df-5586-476d-a11e-28ccba3ddd55", "when": null, @@ -218,7 +218,7 @@ }, "5": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2", + "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18", "errors": null, "id": 5, "input_connections": { @@ -254,15 +254,15 @@ "top": 442.2276665604545 }, "post_job_actions": {}, - "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.17.2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.18", "tool_shed_repository": { - "changeset_revision": "64f11cf59c6e", + "changeset_revision": "2477830927ec", "name": "bwa", "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"analysis_type\": {\"analysis_type_selector\": \"full\", \"__current_case__\": 4, \"algorithmic_options\": {\"algorithmic_options_selector\": \"do_not_set\", \"__current_case__\": 1}, \"scoring_options\": {\"scoring_options_selector\": \"do_not_set\", \"__current_case__\": 1}, \"io_options\": {\"io_options_selector\": \"set\", \"__current_case__\": 0, \"five\": false, \"q\": true, \"T\": \"30\", \"h\": \"5\", \"a\": false, \"C\": false, \"V\": false, \"Y\": true, \"M\": false}}, \"fastq_input\": {\"fastq_input_selector\": \"paired_collection\", \"__current_case__\": 2, \"fastq_input1\": {\"__class__\": \"ConnectedValue\"}, \"iset_stats\": \"\"}, \"output_sort\": \"coordinate\", \"reference_source\": {\"reference_source_selector\": \"history\", \"__current_case__\": 1, \"ref_file\": {\"__class__\": \"ConnectedValue\"}, \"index_a\": \"auto\"}, \"rg\": {\"rg_selector\": \"set\", \"__current_case__\": 1, \"read_group_id_conditional\": {\"do_auto_name\": true, \"__current_case__\": 0}, \"read_group_sm_conditional\": {\"do_auto_name\": true, \"__current_case__\": 0}, \"PL\": \"ILLUMINA\", \"read_group_lb_conditional\": {\"do_auto_name\": true, \"__current_case__\": 0}, \"CN\": null, \"DS\": null, \"DT\": null, \"FO\": null, \"KS\": null, \"PG\": null, \"PI\": null, \"PU\": null}, \"__page__\": null, \"__rerun_remap_job_id__\": null}", - 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"tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.2", + "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0", "tool_shed_repository": { - "changeset_revision": "a1f0b3f4b781", + "changeset_revision": "3f254c5ced1d", "name": "picard", "owner": "devteam", "tool_shed": "toolshed.g2.bx.psu.edu" }, "tool_state": "{\"assume_sorted\": true, \"barcode_tag\": \"\", \"comments\": [], \"duplicate_scoring_strategy\": \"SUM_OF_BASE_QUALITIES\", \"inputFile\": {\"__class__\": \"ConnectedValue\"}, \"optical_duplicate_pixel_distance\": \"100\", \"read_name_regex\": \"\", \"remove_duplicates\": true, \"validation_stringency\": \"LENIENT\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "2.18.2.2", + "tool_version": "3.1.1.0", "type": "tool", "uuid": "32e3534c-283c-45a3-845e-edadfe29343a", "when": null, @@ -399,7 +399,7 @@ }, "9": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", "errors": null, "id": 9, "input_connections": { @@ -420,13 +420,13 @@ "label": null, "name": "MultiQC", "outputs": [ - { - "name": "stats", - "type": "input" - }, { "name": "html_report", "type": "html" + }, + { + "name": "stats", + "type": "tabular" } ], "position": { @@ -447,15 +447,15 @@ "output_name": "html_report" } }, - "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy0", + "tool_id": "toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0", "tool_shed_repository": { - "changeset_revision": "9a913cdee30e", + "changeset_revision": "f7e2f1eb3a16", "name": "multiqc", "owner": "iuc", "tool_shed": "toolshed.g2.bx.psu.edu" }, - "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastp\", \"__current_case__\": 7, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"samtools\", \"__current_case__\": 24, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"stats\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}}]}}, {\"__index__\": 2, \"software_cond\": {\"software\": \"picard\", \"__current_case__\": 17, \"output\": [{\"__index__\": 0, \"type\": \"markdups\", \"input\": {\"__class__\": \"ConnectedValue\"}}]}}], \"saveLog\": false, \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", - "tool_version": "1.11+galaxy0", + "tool_state": "{\"comment\": \"\", \"export\": false, \"flat\": false, \"results\": [{\"__index__\": 0, \"software_cond\": {\"software\": \"fastp\", \"__current_case__\": 7, \"input\": {\"__class__\": \"ConnectedValue\"}}}, {\"__index__\": 1, \"software_cond\": {\"software\": \"samtools\", \"__current_case__\": 24, \"output\": [{\"__index__\": 0, \"type\": {\"type\": \"stats\", \"__current_case__\": 0, \"input\": {\"__class__\": \"ConnectedValue\"}}}]}}, {\"__index__\": 2, \"software_cond\": {\"software\": \"picard\", \"__current_case__\": 17, \"output\": [{\"__index__\": 0, \"type\": \"markdups\", \"input\": {\"__class__\": \"ConnectedValue\"}}]}}], \"saveLog\": \"false\", \"title\": \"\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "1.24.1+galaxy0", "type": "tool", "uuid": "827f0bc5-b7b3-472f-95fc-5bf34fffb9fd", "when": null, @@ -604,7 +604,7 @@ }, "13": { "annotation": "", - "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/4.3+T.galaxy2", + "content_id": "toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/5.2+galaxy0", "errors": null, "id": 13, "input_connections": { @@ -656,15 +656,15 @@ "output_name": "snpeff_output" } }, - 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"tool_version": "4.3+T.galaxy2", + "tool_state": "{\"annotations\": [\"-formatEff\", \"-classic\"], \"chr\": \"\", \"csvStats\": false, \"filter\": {\"specificEffects\": \"no\", \"__current_case__\": 0}, \"filterOut\": [\"-no-downstream\", \"-no-intergenic\", \"-no-intron\", \"-no-upstream\", \"-no-utr\"], \"generate_stats\": true, \"input\": {\"__class__\": \"ConnectedValue\"}, \"inputFormat\": \"vcf\", \"intervals\": {\"__class__\": \"RuntimeValue\"}, \"noLog\": true, \"offset\": \"default\", \"outputConditional\": {\"__current_case__\": 0, \"outputFormat\": \"vcf\"}, \"outputFormat\": \"vcf\", \"snpDb\": {\"genomeSrc\": \"custom\", \"__current_case__\": 3, \"snpeff_db\": {\"__class__\": \"ConnectedValue\"}, \"codon_table\": \"Standard\"}, \"spliceRegion\": {\"setSpliceRegions\": \"no\", \"__current_case__\": 0}, \"spliceSiteSize\": null, \"transcripts\": {\"__class__\": \"RuntimeValue\"}, \"udLength\": \"0\", \"__page__\": null, \"__rerun_remap_job_id__\": null}", + "tool_version": "5.2+galaxy0", "type": "tool", "uuid": "e3d2c332-c029-463c-bb8b-771716db7d67", "when": null, @@ -781,4 +781,4 @@ ], "uuid": "d5b4eace-d876-4999-bad3-14c1cb02b0c9", "version": 5 -} +} \ No newline at end of file