Bulk update of nf-core modules

[lbeltrame]

Should be safe, but one never knows.

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the pipeline conventions in the contribution docs
• Make sure your code lints (nf-core pipelines lint).
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[github-actions]

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 271aa69

+| ✅ 236 tests passed       |+
#| ❔  22 tests were ignored |#
!| ❗  18 tests had warnings |!

❗ Test warnings:

• files_exist - File not found: conf/igenomes_ignored.config
• nextflow_config - nf-validation has been detected in the pipeline. Please migrate to nf-schema: https://nextflow-io.github.io/nf-schema/latest/migration_guide/
• 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 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 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 output.md: Write this documentation describing your workflow's output
• pipeline_todos - TODO string in main.nf.test: Once you have added the required tests, please run the following command to build this file:
• schema_description - No description provided in schema for parameter: purity
• schema_description - No description provided in schema for parameter: max_fragmentsize
• schema_description - No description provided in schema for parameter: ichorcna_male_chrX_logR
• schema_description - No description provided in schema for parameter: ichorcna_filter_bam_pon
• schema_description - No description provided in schema for parameter: wisecondorx_yfrac
• schema_description - No description provided in schema for parameter: ascat_sc_max_tumor_ploidy
• included_configs - Pipeline config does not include custom configs. Please add the includeConfig line.

❔ Tests ignored:

• files_exist - File is ignored: CODE_OF_CONDUCT.md
• files_exist - File is ignored: assets/samurai_logo_mqc.png
• files_exist - File is ignored: assets/nf-core-samurai_logo_light.png
• files_exist - File is ignored: docs/images/nf-core-samurai_logo_light.png
• files_exist - File is ignored: docs/images/nf-core-samurai_logo_dark.png
• files_exist - File is ignored: docs/images/samurai_logo.png
• files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
• files_exist - File is ignored: .github/workflows/awstest.yml
• files_exist - File is ignored: .github/workflows/awsfulltest.yml
• files_exist - File is ignored: .github/workflows/ci.yml
• files_exist - File is ignored: .github/workflows/branch.yml
• nextflow_config - Config variable ignored: manifest.name
• nextflow_config - Config variable ignored: manifest.homePage
• files_unchanged - File does not exist: CODE_OF_CONDUCT.md
• files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
• files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
• files_unchanged - File does not exist: assets/nf-core-samurai_logo_light.png
• files_unchanged - File does not exist: docs/images/nf-core-samurai_logo_light.png
• files_unchanged - File does not exist: docs/images/nf-core-samurai_logo_dark.png
• actions_ci - actions_ci
• actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/samurai/samurai/.github/workflows/awstest.yml
• schema_params - schema_params

✅ 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: 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/feature_request.yml
• files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
• 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: conf/modules.config
• files_exist - File found: conf/test.config
• files_exist - File found: conf/test_full.config
• 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: 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-samurai_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/WorkflowSamurai.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 - Found nf-validation plugin
• 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: 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: 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 variable (correctly) not found: params.max_cpus
• nextflow_config - Config variable (correctly) not found: params.max_memory
• nextflow_config - Config variable (correctly) not found: params.max_time
• 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 dag.file ended with .html
• nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
• nextflow_config - Config manifest.version does not contain dev for release: 1.2.3.1
• 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.genome= hg38
• nextflow_config - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes
• 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.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.purity= 1
• nextflow_config - Config default value correct: params.title= Fragment size distribution
• nextflow_config - Config default value correct: params.max_fragmentsize= 400
• nextflow_config - Config default value correct: params.binsize= 500
• nextflow_config - Config default value correct: params.caller= qdnaseq
• nextflow_config - Config default value correct: params.analysis_type= solid_biopsy
• nextflow_config - Config default value correct: params.qdnaseq_paired_ends= true
• nextflow_config - Config default value correct: params.pon_name= PoN
• nextflow_config - Config default value correct: params.selection_maxsize= 150
• nextflow_config - Config default value correct: params.ichorcna_genome_style= UCSC
• nextflow_config - Config default value correct: params.ichorcna_readcounter_chrs= chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22
• nextflow_config - Config default value correct: params.ichorcna_readcounter_quality= 20
• nextflow_config - Config default value correct: params.ichorcna_chrs_to_use= paste0('chr', c(1:22))
• nextflow_config - Config default value correct: params.ichorcna_chrs_to_train= paste0('chr', c(1:22))
• nextflow_config - Config default value correct: params.ichorcna_chrs_to_normalize= paste0('chr', c(1:22))
• nextflow_config - Config default value correct: params.ichorcna_estimate_normal= TRUE
• nextflow_config - Config default value correct: params.ichorcna_fraction_reads_male= 0.001
• nextflow_config - Config default value correct: params.ichorcna_male_chrX_logR= 0.3
• nextflow_config - Config default value correct: params.ichorcna_min_map_score= 0.75
• nextflow_config - Config default value correct: params.ichorcna_max_frac_genome_subclone= 0.5
• nextflow_config - Config default value correct: params.ichorcna_max_frac_cna_subclone= 0.7
• nextflow_config - Config default value correct: params.ichorcna_min_segment_bins= 50
• nextflow_config - Config default value correct: params.ichorcna_max_cn= 5
• nextflow_config - Config default value correct: params.ichorcna_include_homd= FALSE
• nextflow_config - Config default value correct: params.ichorcna_txne= 0.9999
• nextflow_config - Config default value correct: params.ichorcna_alt_frac_threshold= 0.05
• nextflow_config - Config default value correct: params.ichorcna_trx_strength= 10000
• nextflow_config - Config default value correct: params.ichorcna_plotfiletype= pdf
• nextflow_config - Config default value correct: params.ichorcna_plotylim= c(-2,4)
• nextflow_config - Config default value correct: params.ichorcna_estimate_ploidy= true
• nextflow_config - Config default value correct: params.ichorcna_normal_states= 0.5, 0.6, 0.7, 0.8, 0.9, 0.95, 0.99
• nextflow_config - Config default value correct: params.wisecondorx_yfrac= 0.4
• nextflow_config - Config default value correct: params.wisecondorx_zscore= 5
• nextflow_config - Config default value correct: params.ascat_sc_predict_refit= TRUE
• nextflow_config - Config default value correct: params.ascat_sc_segmentation_alpha= 0.01
• nextflow_config - Config default value correct: params.ascat_sc_min_purity= 0.01
• nextflow_config - Config default value correct: params.ascat_sc_max_purity= 1
• nextflow_config - Config default value correct: params.ascat_sc_min_ploidy= 1.7
• nextflow_config - Config default value correct: params.ascat_sc_max_ploidy= 5
• nextflow_config - Config default value correct: params.ascat_sc_max_tumor_ploidy= 5
• nextflow_config - Config default value correct: params.gistic_t_amp= 0.1
• nextflow_config - Config default value correct: params.gistic_t_del= 0.1
• nextflow_config - Config default value correct: params.gistic_conf= 0.99
• nextflow_config - Config default value correct: params.gistic_qval= 0.05
• nextflow_config - Config default value correct: params.gistic_broad_chr_length= 0.99
• nextflow_config - Config default value correct: params.gistic_cn_cap= 6
• nextflow_config - Config default value correct: params.fastp_cut_window_size= 4
• nextflow_config - Config default value correct: params.hrdcna_threshold= 0.2
• files_unchanged - .gitattributes matches the template
• files_unchanged - .prettierrc.yml 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/feature_request.yml matches the template
• files_unchanged - .github/PULL_REQUEST_TEMPLATE.md 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 - docs/README.md matches the template
• files_unchanged - .gitignore matches the template
• files_unchanged - .prettierignore matches the template
• readme - README Zenodo placeholder was replaced with DOI.
• plugin_includes - No wrong validation plugin imports have been found
• pipeline_name_conventions - Name adheres to nf-core convention
• template_strings - Did not find any Jinja template strings (0 files)
• schema_lint - Schema lint passed
• schema_lint - Schema title + description lint passed
• schema_lint - Input mimetype lint passed: 'text/csv'
• system_exit - No System.exit calls found
• actions_schema_validation - Workflow validation passed: ci.yml
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: linting_comment.yml
• actions_schema_validation - Workflow validation passed: fix-linting.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 'export_plots: true'.
• modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
• base_config - conf/base.config found and not ignored.
• base_config - CUSTOM_DUMPSOFTWAREVERSIONS found in conf/base.config and Nextflow scripts.
• modules_config - conf/modules.config found and not ignored.
• modules_config - FASTQC found in conf/modules.config and Nextflow scripts.
• modules_config - FASTP found in conf/modules.config and Nextflow scripts.
• modules_config - BWA_INDEX found in conf/modules.config and Nextflow scripts.
• modules_config - BWA_MEM found in conf/modules.config and Nextflow scripts.
• modules_config - BWAMEM2_INDEX found in conf/modules.config and Nextflow scripts.
• modules_config - BWAMEM2_MEM found in conf/modules.config and Nextflow scripts.
• modules_config - PICARD_MARKDUPLICATES found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_INDEX found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_IDXSTATS found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_FLAGSTAT found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_STATS found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_VIEW found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_INDEX_SIZE_SELECTION found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_STATS_PRE found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_STATS_POST found in conf/modules.config and Nextflow scripts.
• modules_config - BAMPE_FRAGMENTSIZE_PRE found in conf/modules.config and Nextflow scripts.
• modules_config - BAMPE_FRAGMENTSIZE_POST found in conf/modules.config and Nextflow scripts.
• modules_config - QDNASEQ found in conf/modules.config and Nextflow scripts.
• modules_config - CREATE_QDNASEQ_SUMMARY found in conf/modules.config and Nextflow scripts.
• modules_config - HMMCOPY_READCOUNTER_ICHORCNA found in conf/modules.config and Nextflow scripts.
• modules_config - HMMCOPY_READCOUNTER_PON found in conf/modules.config and Nextflow scripts.
• modules_config - ICHORCNA_GENERATE_PON found in conf/modules.config and Nextflow scripts.
• modules_config - RUN_ICHORCNA found in conf/modules.config and Nextflow scripts.
• modules_config - AGGREGATE_ICHORCNA_TABLE found in conf/modules.config and Nextflow scripts.
• modules_config - CORRECT_LOGR_ICHORCNA found in conf/modules.config and Nextflow scripts.
• modules_config - PLOT_ICHORCNA found in conf/modules.config and Nextflow scripts.
• modules_config - CONCATENATE_QDNASEQ_PLOTS found in conf/modules.config and Nextflow scripts.
• modules_config - NORMAL_CONVERT found in conf/modules.config and Nextflow scripts.
• modules_config - WISECONDORX_CONVERT found in conf/modules.config and Nextflow scripts.
• modules_config - WISECONDORX_NEWREF found in conf/modules.config and Nextflow scripts.
• modules_config - WISECONDORX_PREDICT found in conf/modules.config and Nextflow scripts.
• modules_config - CONVERT_GISTIC_SEG found in conf/modules.config and Nextflow scripts.
• modules_config - ASSEMBLE_WISECONDORX_OUTPUTS found in conf/modules.config and Nextflow scripts.
• modules_config - CONVERT_WISECONDORX_IMAGES found in conf/modules.config and Nextflow scripts.
• modules_config - ASCAT_SC found in conf/modules.config and Nextflow scripts.
• modules_config - CONCATENATE_BIN_PLOTS found in conf/modules.config and Nextflow scripts.
• modules_config - CONCATENATE_ASCATSC_PLOTS found in conf/modules.config and Nextflow scripts.
• modules_config - CONCATENATE_ASCATSC_REFITTED_PLOTS found in conf/modules.config and Nextflow scripts.
• modules_config - CREATE_ASCATSC_SUMMARY found in conf/modules.config and Nextflow scripts.
• modules_config - CIN_SIGNATURE_QUANTIFICATION found in conf/modules.config and Nextflow scripts.
• modules_config - HRDCNA found in conf/modules.config and Nextflow scripts.
• modules_config - GISTIC2 found in conf/modules.config and Nextflow scripts.
• modules_config - ASSEMBLE_GISTIC_OUTPUT found in conf/modules.config and Nextflow scripts.
• modules_config - MAFTOOLS found in conf/modules.config and Nextflow scripts.
• modules_config - CUSTOM_DUMPSOFTWAREVERSIONS 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: 3.0.2
• version_consistency - Version tags are numeric and consistent between container, release tag and config.

Run details

• nf-core/tools version 3.0.2
• Run at 2025-11-04 09:46:42