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WIP: Fix warning nf corelint #1955

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@maxulysse maxulysse commented Aug 14, 2025 •
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Replaces fully #1911
Overlaps a bit with #1912

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/sarek 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).

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github-actions bot commented Aug 14, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 7b36a21

+| ✅ 228 tests passed       |+
#| ❔  10 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

  • 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!

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.3.2
  • Run at 2025-08-19 13:58:02

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tests warnings: 258 -> 129

@maxulysse maxulysse changed the title Fix warning nf corelint WIP: Fix warning nf corelint Aug 14, 2025
@maxulysse maxulysse mentioned this pull request Aug 15, 2025
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@maxulysse maxulysse force-pushed the fix_warning_nf-corelint branch from dad9403 to c535870 Compare August 18, 2025 10:20
maxulysse
maxulysse commented Aug 18, 2025
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solving conflicts locally, as there's a complex snapshot merge conflict involved

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@FriederikeHanssen FriederikeHanssen Awaiting requested review from FriederikeHanssen FriederikeHanssen is a code owner

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