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fix --metadata_category #451

Merged
merged 4 commits into from
Jun 13, 2022
Merged

fix --metadata_category #451

merged 4 commits into from
Jun 13, 2022

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d4straub
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@d4straub d4straub commented Jun 13, 2022 •
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Closes #447

While making sure that --metadata_category propagates to all relevant processes correctly (which was before not given), I changed ch_metacolumn_all & ch_metacolumn_pairwise to contain one value per channel entry instead of one comma separated channel entry. The latter than also means that parallelization is maximized. I touched here code from the very beginning of ampliseq and I hope it did improve overall.

Edit: because the tests fail due to container problems I also fixed nf-core/mag#315 that followed nf-core/rnaseq#764.

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>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
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  • README.md is updated (including new tool citations and authors/contributors).

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github-actions bot commented Jun 13, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 4211134

+| ✅ 147 tests passed       |+
#| ❔   1 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 2.4.1
  • Run at 2022-06-13 14:29:51

ggabernet
ggabernet approved these changes Jun 13, 2022
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Looks good to me

@d4straub d4straub merged commit 9e32930 into nf-core:dev Jun 13, 2022
@d4straub d4straub deleted the fix-metadata_category branch June 13, 2022 14:52
@d4straub d4straub mentioned this pull request Nov 22, 2022
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@ggabernet ggabernet ggabernet approved these changes

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