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Fix missing library #809

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merged 2 commits into from
Dec 3, 2024

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erikrikarddaniel
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@erikrikarddaniel erikrikarddaniel commented Nov 29, 2024

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 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).

Issue #808 reports a missing R library declaration in the FORMAT_PPLACETAX module. I couldn't reproduce the error, but the code does not look like it should work, so I fixed it anyway.

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This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @erikrikarddaniel,

It looks like this pull-request is has been made against the erikrikarddaniel/ampliseq master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the erikrikarddaniel/ampliseq dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

@erikrikarddaniel erikrikarddaniel changed the base branch from master to dev November 29, 2024 15:24
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@d4straub d4straub left a comment

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Thanks! I assume the tests never execute that step because the condition is never met and therefore dont catch the issue. Not sure though.

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That was my guess too, it's just that it looks unlikely (nrow(temp) == 1, but maybe we have a very small test case). Hopefully it works now, but it's not tested.

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CI tests are also passing... hm the test set seems to lack indeed :D

@erikrikarddaniel erikrikarddaniel merged commit e17ab62 into nf-core:dev Dec 3, 2024
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@erikrikarddaniel erikrikarddaniel deleted the fix-missing-library branch December 3, 2024 06:49
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2 participants