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Template update: nf-core/tools version 4.1.0 - #542

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Template update: nf-core/tools version 4.1.0#542
Kevin-Brockers wants to merge 3 commits into
nf-core:devfrom
Kevin-Brockers:dev

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@Kevin-Brockers

@Kevin-Brockers Kevin-Brockers commented Oct 9, 2026

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PR checklist

Since this is my first nf-core template merge, I did the merge on my local fork to not break things.

  • 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/chipseq 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

github-actions Bot commented Oct 9, 2026

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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 4fd2b4a

+| ✅ 271 tests passed       |+
#| ❔   5 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗   9 tests had warnings |!
Details

❗ Test warnings:

  • pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
  • pipeline_todos - TODO string in nextflow.config: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
  • pipeline_todos - TODO string in CHANGELOG.md: ## v2.2.0dev - [unreleased replace with date on release ]
  • 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 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 base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in CONTRIBUTING.md: Add any pipeline specific contribution guidelines here, such as coding styles, procedures, checklists etc.

❔ Tests ignored:

  • nextflow_config - Config default ignored: params.bamtools_filter_pe_config
  • nextflow_config - Config default ignored: params.bamtools_filter_se_config
  • files_unchanged - File ignored due to lint config: assets/nf-core-chipseq_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-chipseq_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore

❔ Tests fixed:

✅ Tests passed:

Run details

  • nf-core/tools version 4.1.0
  • Run at 2026-10-09 17:36:44

@Kevin-Brockers Kevin-Brockers changed the title Template update for nf-core/tools version 4.1.0 Template update: nf-core/tools version 4.1.0 Oct 9, 2026
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@Kevin-Brockers @nf-core-bot