8000 feat: add formula and contrasts to limma by atrigila · Pull Request #8429 · nf-core/modules · GitHub
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feat: add formula and contrasts to limma #8429

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@atrigila atrigila commented May 9, 2025 •
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nf-core/differentialabundance#458

PR checklist

Closes #XXX

  • This comment con 8000 tains 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 module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Emit the versions.yml file.
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • Add a resource label
  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • For modules:
      • nf-core modules test <MODULE> --profile docker
      • nf-core modules test <MODULE> --profile singularity
      • nf-core modules test <MODULE> --profile conda
    • For subworkflows:
      • nf-core subworkflows test <SUBWORKFLOW> --profile docker
      • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
      • nf-core subworkflows test <SUBWORKFLOW> --profile conda

@atrigila atrigila requested a review from grst May 12, 2025 13:26
@atrigila atrigila marked this pull request as ready for review May 12, 2025 13:26
@atrigila atrigila requested a review from pinin4fjords as a code owner May 12, 2025 13:26
pinin4fjords
pinin4fjords reviewed May 13, 2025
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@atrigila atrigila marked this pull request as draft May 14, 2025 18:48
@atrigila atrigila marked this pull request as ready for review May 20, 2025 17:40
@atrigila atrigila requested a review from pinin4fjords May 20, 2025 18:08
grst
grst reviewed May 21, 2025
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Regarding formatting: would it make sense to simply run air on the code once? Maybe the diff would increase, but at least we wouldn't discuss indentation of individual brackets in this PR review.

pinin4fjords
pinin4fjords approved these changes May 22, 2025
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Looking good to me, once @grst 's feedback is addressed. Leaving my green tick so you're not waiting for it.

@atrigila atrigila requested a review from grst May 22, 2025 14:11
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@pinin4fjords pinin4fjords pinin4fjords approved these changes

@grst grst Awaiting requested review from grst

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@atrigila @pinin4fjords @grst
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