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fix vsearch cluster filtering #715

Merged
merged 2 commits into from
Mar 25, 2024
Merged

fix vsearch cluster filtering #715

merged 2 commits into from
Mar 25, 2024

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d4straub
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@d4straub d4straub commented Mar 20, 2024 •
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Closes #696

I have not confirmed myself whether that change allows for more clusters to pass.

My python skills are horrible, so I need some serious opinion whether that seems fine. Tests pass and test files seem fine as well.

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/ampliseq 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 Mar 20, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 583deca

+| ✅ 191 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-03-20 16:02:22

@d4straub d4straub requested review from a4000 and danilodileo March 20, 2024 14:13
erikrikarddaniel
erikrikarddaniel reviewed Mar 20, 2024
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As I mentioned on Slack, I'm not competent here either. But by accident I saw a message that could be made clearer, so made a suggestion.

CHANGELOG.md Outdated Show resolved Hide resolved
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Update CHANGELOG.md
583deca 
Co-authored-by: Daniel Lundin <[email protected]>
a4000
a4000 approved these changes Mar 20, 2024
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The changes look good to me

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d4straub commented Mar 25, 2024 •
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Thanks for the reviews! I am currently testing the test_full dataset with the change and hope it passes (with --vsearch_cluster and without the proposed fix it failed).

edit: indeed, it works!

@d4straub d4straub merged commit f4ac5f6 into nf-core:dev Mar 25, 2024
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@d4straub d4straub deleted the fix-vsearch-cluster branch March 25, 2024 11:29
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@a4000 a4000 a4000 approved these changes

@danilodileo danilodileo Awaiting requested review from danilodileo

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@d4straub @erikrikarddaniel @a4000