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fix FORMAT_TAXONOMY_QIIME #503

Merged
merged 2 commits into from
Dec 5, 2022
Merged

fix FORMAT_TAXONOMY_QIIME #503

merged 2 commits into from
Dec 5, 2022

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d4straub
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@d4straub d4straub commented Nov 22, 2022 •
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Addresses #502

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.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions bot commented Nov 22, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit ac17182

+| ✅ 155 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.
  • schema_lint - Parameter input is not defined in the correct subschema (input_output_options)

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.6
  • Run at 2022-12-02 16:42:41

erikrikarddaniel
erikrikarddaniel approved these changes Nov 23, 2022
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Looks good.

@d4straub
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d4straub commented Dec 2, 2022 •
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Thanks for the review, but the change before was unfortunately not the solution. I reverted the container back to 2.3.2 status. This isnt a perfect solution, but I found no other container that can handle all required commands:

tar xzf $f
unzip *seqs.qza
gunzip -c

many contains contain all tools, but the ubuntu container used in 2.4.0 doesn't contain unzip, leading to errors. Other containers do not work with tar xzf, the z isn't available, hinting at a missing gzip/pigz. The container I revert it back to also isn't sustainable but worked for this pipeline fine for a long time.
A mulled container could be the way to go. I found none, creating one might do the trick. I'll do the fast solution here.

@d4straub d4straub merged commit 2b88a26 into nf-core:dev Dec 5, 2022
@d4straub d4straub mentioned this pull request Dec 6, 2022
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@d4straub d4straub deleted the fix-FORMAT_TAXONOMY_QIIME branch January 12, 2023 09:18
@d4straub d4straub mentioned this pull request Dec 20, 2023
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@d4straub @erikrikarddaniel