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Update kaiju2table module #432

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Merged
merged 9 commits into from
Jan 24, 2024
Merged

Update kaiju2table module #432

merged 9 commits into from
Jan 24, 2024

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sofstam
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@sofstam sofstam commented Jan 22, 2024

This PR updates the kaiju2table module in taxprofiler.

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/taxprofiler 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).

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github-actions bot commented Jan 22, 2024 •
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nf-core lint overall result: Passed ✅

Posted for pipeline commit 913a2d7

+| ✅ 164 tests passed       |+

✅ Tests passed:

Run details

  • nf-core/tools version 2.11.1
  • Run at 2024-01-23 16:12:27

jfy133
jfy133 requested changes Jan 23, 2024
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You should bump all Kaiju module versions to make sure each module's output works each other correctly (e.g.., in case the output has changed in the classification in 1.10, so 1.8 may not work with 1.10 2table )

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sofstam commented Jan 23, 2024

Good point! Thanks!

@sofstam sofstam requested a review from jfy133 January 23, 2024 16:15
@sofstam sofstam merged commit c301bd9 into nf-core:dev Jan 24, 2024
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@jfy133 jfy133 jfy133 approved these changes

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

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@sofstam @jfy133 @nf-core-bot
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