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Fix KrakenUniq classified reads output format mismatch#489

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jfy133 merged 5 commits into
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ku-fix
May 21, 2024
Merged

Fix KrakenUniq classified reads output format mismatch#489
jfy133 merged 5 commits into
devfrom
ku-fix

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@jfy133 jfy133 commented May 16, 2024

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Closes #474

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 (nf-test test main.nf.test -profile test,docker).
  • 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).

@jfy133 jfy133 marked this pull request as draft May 16, 2024 11:09
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github-actions Bot commented May 16, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit d5d82b1

+| ✅ 258 tests passed       |+
!| ❗   2 tests had warnings |!
Details

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-05-16 14:08:30

@jfy133 jfy133 marked this pull request as ready for review May 16, 2024 12:16
Midnighter
Midnighter requested changes May 16, 2024
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Made some suggestions for the regex. If you remove the dumps, then this looks very good to me!

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jfy133
jfy133 commented May 16, 2024
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sigh me and my dumps...

thanks @Midnighter ! I will check with the regex more closely when I have a little more time.

My regex-fu is very poor compared to you, for clarification: I took the 'easier' route as the files are what the module produces and should be fixed (so shouldn't deviate much), but overall more security the better - so I will check and ensure your regex works and then accept it 👍

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@jfy133 @Midnighter
Apply suggestions from code review
d5d82b1 
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
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jfy133 commented May 19, 2024 •
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@Midnighter looks like it works as expected 👍 thank you!

image

If you're happy now please give a ✅ and I will merge!

@jfy133 jfy133 requested a review from Midnighter May 19, 2024 18:41
Midnighter
Midnighter reviewed May 19, 2024
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Midnighter approved these changes May 20, 2024
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Thank you for implementing it in the pipeline ☺️

@jfy133 jfy133 merged commit dc285e0 into dev May 21, 2024
@jfy133 jfy133 deleted the ku-fix branch May 21, 2024 06:19
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@Midnighter Midnighter Midnighter approved these changes

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

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

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