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Merge nf-core template 4.1.0 into dev - #472

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jonasscheid merged 4 commits into
nf-core:devfrom
jonasscheid:merge-template-410
Sep 4, 2026
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Merge nf-core template 4.1.0 into dev#472
jonasscheid merged 4 commits into
nf-core:devfrom
jonasscheid:merge-template-410

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@jonasscheid

@jonasscheid jonasscheid commented Sep 3, 2026 •
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Merge the nf-core/tools 4.1.0 template into dev, resolving the conflicts of the automated PR #471.

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/mhcquant branch on the nf-core/test-datasets repository.
  • 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

github-actions Bot commented Sep 3, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit ac53644

+| ✅ 318 tests passed       |+
!| ❗   6 tests had warnings |!
Details

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: conf/igenomes_ignored.config
  • nextflow_config - Config manifest.version should end in dev: 3.2.0
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
  • pipeline_todos - TODO string in CONTRIBUTING.md: Add any pipeline specific contribution guidelines here, such as coding styles, procedures, checklists etc.
  • schema_lint - Input mimetype is missing or empty

✅ Tests passed:

Run details

  • nf-core/tools version 4.1.0
  • Run at 2026-09-03 23:05:34

@jonasscheid @claude
Add CHANGELOG entry for nf-core template 4.1.0 merge
ac53644 
Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01UqGjJGzjof66KPMZeKTvaU
danilodileo
danilodileo approved these changes Sep 4, 2026
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Look's ok if there isn't anything else than a template update!

@jonasscheid

jonasscheid commented Sep 4, 2026

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Thanks, no just template

@jonasscheid
jonasscheid merged commit a66f441 into nf-core:dev Sep 4, 2026
35 of 37 checks passed
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@danilodileo danilodileo danilodileo approved these changes
@marissaDubbelaar marissaDubbelaar Awaiting requested review from marissaDubbelaar marissaDubbelaar is a code owner

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@jonasscheid @danilodileo @nf-core-bot