Important! Template update for nf-core/tools v3.4.1

[maxulysse]

Replaces:

• #287
• #290

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
• [ ] If necessary, also make a PR on the nf-core/cutandrun branch on the nf-core/test-datasets repository.
• [ ] Make sure your code lints (nf-core 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[bot]]

nf-core pipelines lint overall result: Passed :white_check_mark: :warning:

Posted for pipeline commit ce036e0

+| ✅ 306 tests passed       |+
!| ❗  39 tests had warnings |!

:heavy_exclamation_mark: Test warnings:

• 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 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 nextflow.config: Specify any additional parameters here
• schema_description - No description provided in schema for parameter: run_genome_prep
• schema_description - No description provided in schema for parameter: run_cat_fastq
• schema_description - No description provided in schema for parameter: run_trim_galore_fastqc
• schema_description - No description provided in schema for parameter: run_alignment
• schema_description - No description provided in schema for parameter: run_read_filter
• schema_description - No description provided in schema for parameter: run_preseq
• schema_description - No description provided in schema for parameter: run_mark_dups
• schema_description - No description provided in schema for parameter: run_remove_dups
• schema_description - No description provided in schema for parameter: run_remove_linear_dups
• schema_description - No description provided in schema for parameter: run_peak_calling
• schema_description - No description provided in schema for parameter: run_consensus_all
• schema_description - No description provided in schema for parameter: run_reporting
• schema_description - No description provided in schema for parameter: run_deeptools_heatmaps
• schema_description - No description provided in schema for parameter: run_deeptools_qc
• schema_description - No description provided in schema for parameter: run_peak_qc
• schema_description - No description provided in schema for parameter: run_multiqc
• schema_description - No description provided in schema for parameter: run_igv
• schema_description - No description provided in schema for parameter: fragment_size
• local_component_structure - gtf2bed.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - peak_counts.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - samtools_custom_view.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - peak_frip.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - consensus_peaks.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - fastqc_trimgalore.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - extract_fragments.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - prepare_genome.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - peak_qc.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - mark_duplicates_picard.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - extract_metadata_awk.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - prepare_peakcalling.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - samtools_view_sort_stats.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - deeptools_qc.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - align_bowtie2.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - deduplicate_linear.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

:white_check_mark: Tests passed:

• files_exist - File found: .gitattributes
• files_exist - File found: .gitignore
• files_exist - File found: .nf-core.yml
• 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/nf-test.yml
• files_exist - File found: .github/actions/get-shards/action.yml
• files_exist - File found: .github/actions/nf-test/action.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-cutandrun_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-cutandrun_logo_light.png
• files_exist - File found: docs/images/nf-core-cutandrun_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: nf-test.config
• files_exist - File found: tests/default.nf.test
• 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: conf/igenomes_ignored.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 found: ro-crate-metadata.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-cutandrun_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/WorkflowCutandrun.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-schema plugin
• 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: 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 variable (correctly) not found: params.validationFailUnrecognisedParams
• nextflow_config - Config variable (correctly) not found: params.validationLenientMode
• nextflow_config - Config variable (correctly) not found: params.validationSchemaIgnoreParams
• nextflow_config - Config variable (correctly) not found: params.validationShowHiddenParams
• nextflow_config - Config variable (correctly) not found: validation.failUnrecognisedParams
• nextflow_config - Config variable (correctly) not found: validation.failUnrecognisedHeaders
• 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: 3.3.0dev
• 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.outdir= ./results
• nextflow_config - Config default value correct: params.spikein_genome= K12-MG1655
• nextflow_config - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes/
• nextflow_config - Config default value correct: params.clip_r1= 0
• nextflow_config - Config default value correct: params.clip_r2= 0
• nextflow_config - Config default value correct: params.three_prime_clip_r1= 0
• nextflow_config - Config default value correct: params.three_prime_clip_r2= 0
• nextflow_config - Config default value correct: params.trim_nextseq= 0
• nextflow_config - Config default value correct: params.aligner= bowtie2
• nextflow_config - Config default value correct: params.normalisation_c= 10000
• nextflow_config - Config default value correct: params.minimum_alignment_q_score= 20
• nextflow_config - Config default value correct: params.end_to_end= true
• nextflow_config - Config default value correct: params.normalisation_mode= Spikein
• nextflow_config - Config default value correct: params.normalisation_binsize= 50
• nextflow_config - Config default value correct: params.peakcaller= seacr
• nextflow_config - Config default value correct: params.use_control= true
• nextflow_config - Config default value correct: params.extend_fragments= true
• nextflow_config - Config default value correct: params.igg_scale_factor= 0.5
• nextflow_config - Config default value correct: params.seacr_peak_threshold= 0.05
• nextflow_config - Config default value correct: params.seacr_norm= non
• nextflow_config - Config default value correct: params.seacr_stringent= stringent
• nextflow_config - Config default value correct: params.macs2_qvalue= 0.01
• nextflow_config - Config default value correct: params.macs_gsize= 2700000000.0
• nextflow_config - Config default value correct: params.macs2_narrow_peak= true
• nextflow_config - Config default value correct: params.macs2_broad_cutoff= 0.1
• nextflow_config - Config default value correct: params.consensus_peak_mode= group
• nextflow_config - Config default value correct: params.replicate_threshold= 1.0
• nextflow_config - Config default value correct: params.igv_show_gene_names= true
• nextflow_config - Config default value correct: params.dt_qc_bam_binsize= 500
• nextflow_config - Config default value correct: params.dt_qc_corr_method= pearson
• nextflow_config - Config default value correct: params.dt_heatmap_gene_beforelen= 3000
• nextflow_config - Config default value correct: params.dt_heatmap_gene_bodylen= 5000
• nextflow_config - Config default value correct: params.dt_heatmap_gene_afterlen= 3000
• nextflow_config - Config default value correct: params.dt_heatmap_peak_beforelen= 3000
• nextflow_config - Config default value correct: params.dt_heatmap_peak_afterlen= 3000
• nextflow_config - Config default value correct: params.dt_calc_all_matrix= true
• nextflow_config - Config default value correct: params.fragment_size= 100
• nextflow_config - Config default value correct: params.min_frip_overlap= 0.2
• nextflow_config - Config default value correct: params.min_peak_overlap= 0.2
• nextflow_config - Config default value correct: params.igv_sort_by_groups= true
• 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.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/
• nf_test_content - 'tests/default.nf.test' contains outdir parameter
• nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/nextflow.config' contains modules_testdata_base_path
• nf_test_content - 'tests/nextflow.config' contains pipelines_testdata_base_path
• nf_test_content - 'nf-test.config' sets a testsDir
• nf_test_content - 'nf-test.config' sets a workDir
• nf_test_content - 'nf-test.config' sets a configFile
• 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-cutandrun_logo_light.png matches the template
• files_unchanged - docs/images/nf-core-cutandrun_logo_light.png matches the template
• files_unchanged - docs/images/nf-core-cutandrun_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_nf_test - '.github/workflows/nf-test.yml' is triggered on expected events
• actions_nf_test - '.github/workflows/nf-test.yml' checks minimum NF version
• 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: 25.04.0, Config: 25.04.0
• readme - README nf-core template version badge found.
• readme - README Zenodo placeholder was replaced with DOI.
• pipeline_if_empty_null - No ifEmpty(null) strings found
• 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'
• schema_params - Schema matched params returned from nextflow config
• system_exit - No System.exit calls found
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: download_pipeline.yml
• actions_schema_validation - Workflow validation passed: template-version-comment.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: fix_linting.yml
• actions_schema_validation - Workflow validation passed: nf-test.yml
• actions_schema_validation - Workflow validation passed: awsfulltest.yml
• actions_schema_validation - Workflow validation passed: branch.yml
• actions_schema_validation - Workflow validation passed: awstest.yml
• actions_schema_validation - Workflow validation passed: clean-up.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.
• base_config - NFCORE_CUTANDRUN found in conf/base.config and Nextflow scripts.
• base_config - NFCORE_CUTANDRUN found in conf/base.config and Nextflow scripts.
• base_config - NFCORE_CUTANDRUN found in conf/base.config and Nextflow scripts.
• base_config - NFCORE_CUTANDRUN found in conf/base.config and Nextflow scripts.
• base_config - NFCORE_CUTANDRUN found in conf/base.config and Nextflow scripts.
• modules_config - conf/modules.config found and not ignored.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - BOWTIE2_BUILD_ found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - CAT_FASTQ found in conf/modules.config and Nextflow scripts.
• modules_config - FASTQC found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - NFCORE_CUTANDRUN found in conf/modules.config and Nextflow scripts.
• modules_config - MULTIQC 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: 3.4.1
• rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

• nf-core/tools version 3.4.1
• Run at 2025-10-21 12:45:54