Add nf-test #1063

jfy133 · 2024-04-26T08:57:10Z

… test profile

Initial set up, testing command nf-test test --tag test --profile test,docker

PR checklist

… test profile

github-actions · 2024-04-26T08:59:12Z

`nf-core lint` overall result: Passed ✅ ⚠️

Posted for pipeline commit bb12ca1

+| ✅ 361 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗  21 tests had warnings |!

❗ Test warnings:

readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
pipeline_todos - TODO string in README.md: Include a figure that guides the user through the major workflow steps. Many nf-core
pipeline_todos - TODO string in README.md: Fill in short bullet-pointed list of the default steps in the pipeline
pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file
pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
pipeline_todos - TODO string in test_humanbam.config: Specify the paths to your test data on nf-core/test-datasets
pipeline_todos - TODO string in test_humanbam.config: Give any required params for the test so that command line flags are not needed
pipeline_todos - TODO string in test.config: Specify the paths to your test data on nf-core/test-datasets
pipeline_todos - TODO string in test.config: Give any required params for the test so that command line flags are not needed
pipeline_todos - TODO string in test_nothing.config: Specify the paths to your test data on nf-core/test-datasets
pipeline_todos - TODO string in test_nothing.config: Give any required params for the test so that command line flags are not needed
pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
pipeline_todos - TODO string in base.config: Check the defaults for all processes
pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.

❔ Tests ignored:

nextflow_config - Config default ignored: params.contamination_estimation_angsd_hapmap
actions_ci - actions_ci

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .nf-core.yml
files_exist - File found: .editorconfig
files_exist - File found: .prettierignore
files_exist - File found: .prettierrc.yml
files_exist - File found: CHANGELOG.md
files_exist - File found: CITATIONS.md
files_exist - File found: CODE_OF_CONDUCT.md
files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_exist - File found: nextflow_schema.json
files_exist - File found: nextflow.config
files_exist - File found: README.md
files_exist - File found: .github/.dockstore.yml
files_exist - File found: .github/CONTRIBUTING.md
files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.yml
files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.yml
files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
files_exist - File found: .github/workflows/branch.yml
files_exist - File found: .github/workflows/ci.yml
files_exist - File found: .github/workflows/linting_comment.yml
files_exist - File found: .github/workflows/linting.yml
files_exist - File found: assets/email_template.html
files_exist - File found: assets/email_template.txt
files_exist - File found: assets/sendmail_template.txt
files_exist - File found: assets/nf-core-eager_logo_light.png
files_exist - File found: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/images/nf-core-eager_logo_light.png
files_exist - File found: docs/images/nf-core-eager_logo_dark.png
files_exist - File found: docs/output.md
files_exist - File found: docs/README.md
files_exist - File found: docs/README.md
files_exist - File found: docs/usage.md
files_exist - File found: main.nf
files_exist - File found: assets/multiqc_config.yml
files_exist - File found: conf/base.config
files_exist - File found: conf/igenomes.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: modules.json
files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
files_exist - File not found check: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: .yamllint.yml
files_exist - File not found check: bin/markdown_to_html.r
files_exist - File not found check: conf/aws.config
files_exist - File not found check: docs/images/nf-core-eager_logo.png
files_exist - File not found check: lib/Checks.groovy
files_exist - File not found check: lib/Completion.groovy
files_exist - File not found check: lib/NfcoreTemplate.groovy
files_exist - File not found check: lib/Utils.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/WorkflowEager.groovy
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: Singularity
files_exist - File not found check: lib/nfcore_external_java_deps.jar
files_exist - File not found check: .travis.yml
nextflow_config - Config variable found: manifest.name
nextflow_config - Config variable found: manifest.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
nextflow_config - Config variable found: manifest.homePage
nextflow_config - Config variable found: timeline.enabled
nextflow_config - Config variable found: trace.enabled
nextflow_config - Config variable found: report.enabled
nextflow_config - Config variable found: dag.enabled
nextflow_config - Config variable found: process.cpus
nextflow_config - Config variable found: process.memory
nextflow_config - Config variable found: process.time
nextflow_config - Config variable found: params.outdir
nextflow_config - Config variable found: params.input
nextflow_config - Config variable found: params.validationShowHiddenParams
nextflow_config - Config variable found: params.validationSchemaIgnoreParams
nextflow_config - Config variable found: manifest.mainScript
nextflow_config - Config variable found: timeline.file
nextflow_config - Config variable found: trace.file
nextflow_config - Config variable found: report.file
nextflow_config - Config variable found: dag.file
nextflow_config - Config variable (correctly) not found: params.nf_required_version
nextflow_config - Config variable (correctly) not found: params.container
nextflow_config - Config variable (correctly) not found: params.singleEnd
nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
nextflow_config - Config variable (correctly) not found: params.name
nextflow_config - Config variable (correctly) not found: params.enable_conda
nextflow_config - Config timeline.enabled had correct value: true
nextflow_config - Config report.enabled had correct value: true
nextflow_config - Config trace.enabled had correct value: true
nextflow_config - Config dag.enabled had correct value: true
nextflow_config - Config manifest.name began with nf-core/
nextflow_config - Config variable manifest.homePage began with https://github.com/nf-core/
nextflow_config - Config dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config manifest.version ends in dev: 3.0.0dev
nextflow_config - Config params.custom_config_version is set to master
nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Lines for loading custom profiles found
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes/
nextflow_config - Config default value correct: params.fasta_circularmapper_elongationfactor= 500
nextflow_config - Config default value correct: params.custom_config_version= master
nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Config default value correct: params.max_cpus= 16
nextflow_config - Config default value correct: params.max_memory= 128.GB
nextflow_config - Config default value correct: params.max_time= 240.h
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
nextflow_config - Config default value correct: params.validate_params= true
nextflow_config - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/
nextflow_config - Config default value correct: params.sequencing_qc_tool= fastqc
nextflow_config - Config default value correct: params.preprocessing_tool= fastp
nextflow_config - Config default value correct: params.preprocessing_minlength= 25
nextflow_config - Config default value correct: params.preprocessing_trim5p= 0
nextflow_config - Config default value correct: params.preprocessing_trim3p= 0
nextflow_config - Config default value correct: params.preprocessing_fastp_complexityfilter_threshold= 10
nextflow_config - Config default value correct: params.preprocessing_adapterremoval_trimbasequalitymin= 20
nextflow_config - Config default value correct: params.preprocessing_adapterremoval_adapteroverlap= 1
nextflow_config - Config default value correct: params.preprocessing_adapterremoval_qualitymax= 41
nextflow_config - Config default value correct: params.fastq_shard_size= 1000000
nextflow_config - Config default value correct: params.mapping_tool= bwaaln
nextflow_config - Config default value correct: params.mapping_bwaaln_n= 0.01
nextflow_config - Config default value correct: params.mapping_bwaaln_k= 2
nextflow_config - Config default value correct: params.mapping_bwaaln_l= 1024
nextflow_config - Config default value correct: params.mapping_bwaaln_o= 2
nextflow_config - Config default value correct: params.mapping_bwamem_k= 19
nextflow_config - Config default value correct: params.mapping_bwamem_r= 1.5
nextflow_config - Config default value correct: params.mapping_bowtie2_alignmode= local
nextflow_config - Config default value correct: params.mapping_bowtie2_sensitivity= sensitive
nextflow_config - Config default value correct: params.mapping_bowtie2_n= 0
nextflow_config - Config default value correct: params.mapping_bowtie2_l= 20
nextflow_config - Config default value correct: params.mapping_bowtie2_trim5= 0
nextflow_config - Config default value correct: params.mapping_bowtie2_trim3= 0
nextflow_config - Config default value correct: params.mapping_bowtie2_maxins= 500
nextflow_config - Config default value correct: params.bamfiltering_minreadlength= 0
nextflow_config - Config default value correct: params.bamfiltering_mappingquality= 0
nextflow_config - Config default value correct: params.bamfilter_genomicbamfilterflag= 4
nextflow_config - Config default value correct: params.metagenomics_input= unmapped
nextflow_config - Config default value correct: params.metagenomics_complexity_tool= bbduk
nextflow_config - Config default value correct: params.metagenomics_complexity_entropy= 0.3
nextflow_config - Config default value correct: params.metagenomics_prinseq_mode= entropy
nextflow_config - Config default value correct: params.metagenomics_prinseq_dustscore= 0.5
nextflow_config - Config default value correct: params.metagenomics_krakenuniq_ramchunksize= 16G
nextflow_config - Config default value correct: params.metagenomics_malt_mode= BlastN
nextflow_config - Config default value correct: params.metagenomics_malt_alignmentmode= SemiGlobal
nextflow_config - Config default value correct: params.metagenomics_malt_minpercentidentity= 85
nextflow_config - Config default value correct: params.metagenomics_malt_toppercent= 1
nextflow_config - Config default value correct: params.metagenomics_malt_minsupportmode= percent
nextflow_config - Config default value correct: params.metagenomics_malt_minsupportpercent= 0.01
nextflow_config - Config default value correct: params.metagenomics_malt_minsupportreads= 1
nextflow_config - Config default value correct: params.metagenomics_malt_maxqueries= 100
nextflow_config - Config default value correct: params.metagenomics_malt_memorymode= load
nextflow_config - Config default value correct: params.metagenomics_malt_group_size= 0
nextflow_config - Config default value correct: params.metagenomics_maltextract_filter= def_anc
nextflow_config - Config default value correct: params.metagenomics_maltextract_toppercent= 0.01
nextflow_config - Config default value correct: params.metagenomics_maltextract_minpercentidentity= 85.0
nextflow_config - Config default value correct: params.deduplication_tool= markduplicates
nextflow_config - Config default value correct: params.damage_manipulation_rescale_seqlength= 12
nextflow_config - Config default value correct: params.damage_manipulation_rescale_length_5p= 0
nextflow_config - Config default value correct: params.damage_manipulation_rescale_length_3p= 0
nextflow_config - Config default value correct: params.damage_manipulation_pmdtools_threshold= 3
nextflow_config - Config default value correct: params.damage_manipulation_bamutils_trim_double_stranded_none_udg_left= 0
nextflow_config - Config default value correct: params.damage_manipulation_bamutils_trim_double_stranded_none_udg_right= 0
nextflow_config - Config default value correct: params.damage_manipulation_bamutils_trim_double_stranded_half_udg_left= 0
nextflow_config - Config default value correct: params.damage_manipulation_bamutils_trim_double_stranded_half_udg_right= 0
nextflow_config - Config default value correct: params.damage_manipulation_bamutils_trim_single_stranded_none_udg_left= 0
nextflow_config - Config default value correct: params.damage_manipulation_bamutils_trim_single_stranded_none_udg_right= 0
nextflow_config - Config default value correct: params.damage_manipulation_bamutils_trim_single_stranded_half_udg_left= 0
nextflow_config - Config default value correct: params.damage_manipulation_bamutils_trim_single_stranded_half_udg_right= 0
nextflow_config - Config default value correct: params.genotyping_reference_ploidy= 2
nextflow_config - Config default value correct: params.genotyping_pileupcaller_min_base_quality= 30
nextflow_config - Config default value correct: params.genotyping_pileupcaller_min_map_quality= 30
nextflow_config - Config default value correct: params.genotyping_pileupcaller_method= randomHaploid
nextflow_config - Config default value correct: params.genotyping_pileupcaller_transitions_mode= AllSites
nextflow_config - Config default value correct: params.genotyping_gatk_call_conf= 30
nextflow_config - Config default value correct: params.genotyping_gatk_ug_downsample= 250
nextflow_config - Config default value correct: params.genotyping_gatk_ug_out_mode= EMIT_VARIANTS_ONLY
nextflow_config - Config default value correct: params.genotyping_gatk_ug_genotype_mode= SNP
nextflow_config - Config default value correct: params.genotyping_gatk_ug_defaultbasequalities= -1
nextflow_config - Config default value correct: params.genotyping_gatk_hc_out_mode= EMIT_VARIANTS_ONLY
nextflow_config - Config default value correct: params.genotyping_gatk_hc_emitrefconf= GVCF
nextflow_config - Config default value correct: params.genotyping_freebayes_min_alternate_count= 1
nextflow_config - Config default value correct: params.genotyping_freebayes_skip_coverage= 0
nextflow_config - Config default value correct: params.genotyping_angsd_glmodel= samtools
nextflow_config - Config default value correct: params.genotyping_angsd_glformat= binary
nextflow_config - Config default value correct: params.mitochondrion_header= MT
nextflow_config - Config default value correct: params.mapstats_preseq_mode= c_curve
nextflow_config - Config default value correct: params.mapstats_preseq_stepsize= 1000
nextflow_config - Config default value correct: params.mapstats_preseq_terms= 100
nextflow_config - Config default value correct: params.mapstats_preseq_maxextrap= 10000000000
nextflow_config - Config default value correct: params.mapstats_preseq_bootstrap= 100
nextflow_config - Config default value correct: params.mapstats_preseq_cval= 0.95
nextflow_config - Config default value correct: params.damagecalculation_tool= damageprofiler
nextflow_config - Config default value correct: params.damagecalculation_yaxis= 0.3
nextflow_config - Config default value correct: params.damagecalculation_xaxis= 25
nextflow_config - Config default value correct: params.damagecalculation_damageprofiler_length= 100
nextflow_config - Config default value correct: params.damagecalculation_mapdamage_downsample= 0
nextflow_config - Config default value correct: params.host_removal_mode= remove
nextflow_config - Config default value correct: params.contamination_estimation_angsd_chrom_name= X
nextflow_config - Config default value correct: params.contamination_estimation_angsd_range_from= 5000000
nextflow_config - Config default value correct: params.contamination_estimation_angsd_range_to= 154900000
nextflow_config - Config default value correct: params.contamination_estimation_angsd_mapq= 30
nextflow_config - Config default value correct: params.contamination_estimation_angsd_minq= 30
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - CODE_OF_CONDUCT.md matches the template
files_unchanged - LICENSE matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/CONTRIBUTING.md matches the template
files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
files_unchanged - .github/PULL_REQUEST_TEMPLATE.md matches the template
files_unchanged - .github/workflows/branch.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
files_unchanged - .github/workflows/linting.yml matches the template
files_unchanged - assets/email_template.html matches the template
files_unchanged - assets/email_template.txt matches the template
files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - assets/nf-core-eager_logo_light.png matches the template
files_unchanged - docs/images/nf-core-eager_logo_light.png matches the template
files_unchanged - docs/images/nf-core-eager_logo_dark.png matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
readme - README Nextflow minimum version badge matched config. Badge: 23.04.0, Config: 23.04.0
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (440 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_lint - Input mimetype lint passed: 'text/csv'
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
multiqc_config - assets/multiqc_config.yml found and not ignored.
multiqc_config - assets/multiqc_config.yml contains report_section_order
multiqc_config - assets/multiqc_config.yml contains export_plots
multiqc_config - assets/multiqc_config.yml contains report_comment
multiqc_config - assets/multiqc_config.yml follows the ordering scheme of the minimally required plugins.
multiqc_config - assets/multiqc_config.yml contains a matching 'report_comment'.
multiqc_config - assets/multiqc_config.yml contains 'export_plots: true'.
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
modules_config - conf/modules.config found and not ignored.
modules_config - SAMTOOLS_CONVERT_BAM_INPUT found in conf/modules.config and Nextflow scripts.
modules_config - CAT_FASTQ_CONVERTED_BAM found in conf/modules.config and Nextflow scripts.
modules_config - FASTQC found in conf/modules.config and Nextflow scripts.
modules_config - FASTQC_PROCESSED found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
modules_config - FALCO found in conf/modules.config and Nextflow scripts.
modules_config - FALCO_PROCESSED found in conf/modules.config and Nextflow scripts.
modules_config - FASTP_SINGLE found in conf/modules.config and Nextflow scripts.
modules_config - FASTP_PAIRED found in conf/modules.config and Nextflow scripts.
modules_config - ADAPTERREMOVAL_SINGLE found in conf/modules.config and Nextflow scripts.
modules_config - ADAPTERREMOVAL_PAIRED found in conf/modules.config and Nextflow scripts.
modules_config - CAT_FASTQ_ADAPTERREMOVAL found in conf/modules.config and Nextflow scripts.
modules_config - GUNZIP_FASTA found in conf/modules.config and Nextflow scripts.
modules_config - GUNZIP_PMDFASTA found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_FAIDX found in conf/modules.config and Nextflow scripts.
modules_config - PICARD_CREATESEQUENCEDICTIONARY found in conf/modules.config and Nextflow scripts.
modules_config - BOWTIE2_BUILD found in conf/modules.config and Nextflow scripts.
modules_config - BWA_INDEX found in conf/modules.config and Nextflow scripts.
modules_config - GUNZIP_ELONGATED_FASTA found in conf/modules.config and Nextflow scripts.
modules_config - CIRCULARMAPPER_CIRCULARGENERATOR found in conf/modules.config and Nextflow scripts.
modules_config - BWA_INDEX_CIRCULARISED found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_FLAGSTATS_BAM_INPUT found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_INDEX_BAM_INPUT found in conf/modules.config and Nextflow scripts.
modules_config - CAT_FASTQ_UNMAPPED found in conf/modules.config and Nextflow scripts.
modules_config - FILTER_BAM_FRAGMENT_LENGTH found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_FASTQ_UNMAPPED found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_VIEW_BAM_FILTERING found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_LENGTH_FILTER_INDEX found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_FASTQ_MAPPED found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_FLAGSTAT_FILTERED found in conf/modules.config and Nextflow scripts.
modules_config - SEQKIT_SPLIT2 found in conf/modules.config and Nextflow scripts.
modules_config - BWA_ALN found in conf/modules.config and Nextflow scripts.
modules_config - BWA_SAMSE found in conf/modules.config and Nextflow scripts.
modules_config - ENDORSPY found in conf/modules.config and Nextflow scripts.
modules_config - BWA_MEM found in conf/modules.config and Nextflow scripts.
modules_config - BOWTIE2_ALIGN found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_INDEX_MEM found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_MERGE_LANES found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_SORT_MERGED_LANES found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_INDEX_MERGED_LANES found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_FLAGSTAT_MERGED_LANES found in conf/modules.config and Nextflow scripts.
modules_config - CIRCULARMAPPER_REALIGNSAMFILE found in conf/modules.config and Nextflow scripts.
modules_config - PICARD_MARKDUPLICATES found in conf/modules.config and Nextflow scripts.
modules_config - DEDUP found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_MERGE_DEDUPPED found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_SORT_DEDUPPED found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_INDEX_DEDUPPED found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_FLAGSTAT_DEDUPPED found in conf/modules.config and Nextflow scripts.
modules_config - HOST_REMOVAL found in conf/modules.config and Nextflow scripts.
modules_config - PRESEQ_CCURVE found in conf/modules.config and Nextflow scripts.
modules_config - PRESEQ_LCEXTRAP found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_VIEW_GENOME found in conf/modules.config and Nextflow scripts.
modules_config - BEDTOOLS_COVERAGE_DEPTH found in conf/modules.config and Nextflow scripts.
modules_config - BEDTOOLS_COVERAGE_BREADTH found in conf/modules.config and Nextflow scripts.
modules_config - BEDTOOLS_MASKFASTA found in conf/modules.config and Nextflow scripts.
modules_config - MAPDAMAGE2 found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_INDEX_DAMAGE_RESCALED found in conf/modules.config and Nextflow scripts.
modules_config - PMDTOOLS_FILTER found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_INDEX_DAMAGE_FILTERED found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_FLAGSTAT_DAMAGE_FILTERED found in conf/modules.config and Nextflow scripts.
modules_config - BAMUTIL_TRIMBAM found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_INDEX_DAMAGE_TRIMMED found in conf/modules.config and Nextflow scripts.
modules_config - ANGSD_DOCOUNTS found in conf/modules.config and Nextflow scripts.
modules_config - ANGSD_CONTAMINATION found in conf/modules.config and Nextflow scripts.
modules_config - PRINT_CONTAMINATION_ANGSD found in conf/modules.config and Nextflow scripts.
modules_config - MTNUCRATIO found in conf/modules.config and Nextflow scripts.
modules_config - PRINSEQPLUSPLUS found in conf/modules.config and Nextflow scripts.
modules_config - BBMAP_BBDUK found in conf/modules.config and Nextflow scripts.
modules_config - MALT_RUN found in conf/modules.config and Nextflow scripts.
modules_config - CAT_CAT_MALT found in conf/modules.config and Nextflow scripts.
modules_config - KRAKEN2_KRAKEN2 found in conf/modules.config and Nextflow scripts.
modules_config - KRAKENUNIQ_PRELOADEDKRAKENUNIQ found in conf/modules.config and Nextflow scripts.
modules_config - METAPHLAN_METAPHLAN found in conf/modules.config and Nextflow scripts.
modules_config - MALTEXTRACT found in conf/modules.config and Nextflow scripts.
modules_config - MEGAN_RMA2INFO found in conf/modules.config and Nextflow scripts.
modules_config - AMPS found in conf/modules.config and Nextflow scripts.
modules_config - TAXPASTA_MERGE found in conf/modules.config and Nextflow scripts.
modules_config - TAXPASTA_STANDARDISE found in conf/modules.config and Nextflow scripts.
modules_config - QUALIMAP_BAMQC_WITHBED found in conf/modules.config and Nextflow scripts.
modules_config - DAMAGEPROFILER found in conf/modules.config and Nextflow scripts.
modules_config - CALCULATE_MAPDAMAGE2 found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_DEPTH_SEXDETERRMINE found in conf/modules.config and Nextflow scripts.
modules_config - SEXDETERRMINE found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_MPILEUP_PILEUPCALLER found in conf/modules.config and Nextflow scripts.
modules_config - SEQUENCETOOLS_PILEUPCALLER found in conf/modules.config and Nextflow scripts.
modules_config - COLLECT_GENOTYPES found in conf/modules.config and Nextflow scripts.
modules_config - EIGENSTRATDATABASETOOLS_EIGENSTRATSNPCOVERAGE found in conf/modules.config and Nextflow scripts.
modules_config - GATK_REALIGNERTARGETCREATOR found in conf/modules.config and Nextflow scripts.
modules_config - GATK_INDELREALIGNER found in conf/modules.config and Nextflow scripts.
modules_config - GATK_UNIFIEDGENOTYPER found in conf/modules.config and Nextflow scripts.
modules_config - BCFTOOLS_INDEX_UG found in conf/modules.config and Nextflow scripts.
modules_config - GATK4_HAPLOTYPECALLER found in conf/modules.config and Nextflow scripts.
modules_config - FREEBAYES found in conf/modules.config and Nextflow scripts.
modules_config - BCFTOOLS_INDEX_FREEBAYES found in conf/modules.config and Nextflow scripts.
modules_config - BCFTOOLS_STATS_GENOTYPING found in conf/modules.config and Nextflow scripts.
modules_config - ANGSD_GL found in conf/modules.config and Nextflow scripts.
nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 2.14.1

Run details

nf-core/tools version 2.14.1
Run at 2024-10-04 10:21:44

jfy133 · 2024-04-26T09:17:54Z

jfy133 · 2024-06-28T08:57:14Z

Existing tests to make sure we account for with new configs:

          - "-profile test,docker --preprocessing_tool fastp --preprocessing_adapterlist 'https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/fastp/adapters.fasta'"
          - "-profile test,docker --preprocessing_tool adapterremoval --preprocessing_adapterlist 'https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/adapterremoval/adapterremoval_adapterlist.txt' --sequencing_qc_tool falco --run_genotyping --genotyping_tool 'freebayes' --genotyping_source 'raw'"
          - "-profile test,docker --mapping_tool bwamem --run_mapdamage_rescaling --run_pmd_filtering --run_trim_bam --run_genotyping --genotyping_tool 'ug' --genotyping_source 'trimmed'"
          - "-profile test,docker --mapping_tool bowtie2 --damagecalculation_tool mapdamage --damagecalculation_mapdamage_downsample 100 --run_genotyping --genotyping_tool 'hc' --genotyping_source 'raw'"
          - "-profile test,docker --skip_preprocessing --convert_inputbam"
          - "-profile test_humanbam,docker --run_mtnucratio --run_contamination_estimation_angsd --snpcapture_bed 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/reference/Human/1240K.pos.list_hs37d5.0based.bed.gz' --run_genotyping --genotyping_tool 'pileupcaller' --genotyping_source 'raw'"
          - "-profile test_humanbam,docker --run_sexdeterrmine --run_genotyping --genotyping_tool 'angsd' --genotyping_source 'raw'"
          - "-profile test_multiref,docker" ## TODO add damage manipulation here instead once it goes multiref

…roblem with collection/name not working

…Dir (but not working - no md5swum?!)

jfy133 · 2024-07-20T07:30:43Z

Ok, just need to sort the lists and then it should work (md5sums are the same but just seem to be out of order)

…ability

nf-core/eager#1063 Co-authored-by: jfy133 <[email protected]> Co-authored-by: nvnieuwk <[email protected]>

…nk so

jfy133 · 2024-09-20T10:44:35Z

I thought I had pulled in the latest dev branch but I'm getting differing output when it's running online with GHA, I might need to debug the cuases of the differences more closely (maybe add --verbose --debug) ?

TCLamnidis · 2024-12-04T15:09:20Z

Somehow the results from mapping are not picked up by nf-test, and I'm at a loss. might need a fresh pair of eyes...

Fix snapshot of mapping process (not picking up any files atm)
Add MultiQC
Add final_bams
Double-check that all results are snapshotted

jfy133 · 2024-12-05T09:05:44Z

Side note: when I was looking to test, maybe the flagstat files that currently falling in mapping/bwaaln/*flagstat should go into mapstats/ ?

Add general structure, and generate (not working!) snapshot for basic…

f7fceaf

… test profile

jfy133 marked this pull request as draft April 26, 2024 08:57

jfy133 added 2 commits April 26, 2024 13:00

Try adding an ignore zip system, doesn't work atm though...

0778e58

Merge branch 'dev' into nf-test-conversionMerge in from dev

eb73ae6

jfy133 added 10 commits June 28, 2024 13:40

Continue customisation

cc114f3

More debugging

37994df

Get working function

e07dc06

Get working function properly, and start integrating into snapshot: p…

c0f93d9

…roblem with collection/name not working

Extract names properly

de035ca

Remove unnecesary code

7890575

Get working string check function!

b795b9e

TODO

cac8152

Update MQC so works on gitpod, try to re-add original getAllFilesFrom…

a8dcd64

…Dir (but not working - no md5swum?!)

And get it back again

56cba0c

jfy133 added 6 commits July 22, 2024 08:51

Sort output to ensure consistency

0f12b21

Sort file name only funciton

d41aad9

Start testing preprocessing

61c4d24

Merge branch 'dev' into nf-test-conversion

19db88c

Start adding preprocessing dir but diff not working so can't ser vari…

bcc3baf

…ability

Backing up TODO notes

0b58cf7

edmundmiller added a commit to nf-core/nascent that referenced this pull request Aug 10, 2024

test: Add UTILS functions from function guy

4026329

nf-core/eager#1063 Co-authored-by: jfy133 <[email protected]> Co-authored-by: nvnieuwk <[email protected]>

edmundmiller added a commit to nf-core/nascent that referenced this pull request Aug 10, 2024

test: Add UTILS functions from function guy

f5aa9e1

nf-core/eager#1063 Co-authored-by: jfy133 <[email protected]> Co-authored-by: nvnieuwk <[email protected]>

edmundmiller added a commit to nf-core/nascent that referenced this pull request Aug 11, 2024

test: Add UTILS functions from function guy

2d049ff

nf-core/eager#1063 Co-authored-by: jfy133 <[email protected]> Co-authored-by: nvnieuwk <[email protected]>

Final snapshots, need to double check all files are covered but I thi…

eb4824e

…nk so

TCLamnidis added this to the 3.0 Augsburg milestone Sep 6, 2024

Finalise first test

9ce930f

jfy133 added 2 commits September 20, 2024 11:11

Merge branch 'dev' into nf-test-conversion

5598eec

Update tests to latest dev

6362fa3

jfy133 added 3 commits October 4, 2024 11:39

Merge branch 'dev' into nf-test-conversion

61086b5

Merge branch 'dev' into nf-test-conversion

9a56d48

Start refactoring to use nft-utils

bb12ca1

TCLamnidis assigned jfy133 and TCLamnidis Oct 4, 2024

TCLamnidis added 14 commits October 11, 2024 10:52

fix qualimap output dir typo

87fafc5

no sampleid in qualimap outdir

ef71d3b

bump nft-utils version

a7fadc6

start refactoring to use nft-utils

4baefaf

update snapshot. Not sure it works yet.

8b7e950

add preprocessing

2e5bf4f

fix preprocessing checks

c204fe9

Merge remote-tracking branch 'origin/dev' into nf-test-conversion

4efc86b

Merge remote-tracking branch 'origin/dev' into nf-test-conversion

9f3611f

reorder and add todos

6893eb6

remove versions.ymls from snapshot

13a640c

check bam names instead of content

5241ffc

add ave_filtered_bam parameter to test profile

0dab178

fix result pickup for bam filtering and deduplication

01850ad

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Add nf-test #1063

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nf-core lint overall result: Passed ✅ ⚠️

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Variable output

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`nf-core lint` overall result: Passed ✅ ⚠️

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