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Fix --*_ref_taxonomy validation #769

Merged
merged 5 commits into from
Jul 25, 2024
Merged

Fix --*_ref_taxonomy validation #769

merged 5 commits into from
Jul 25, 2024

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d4straub
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@d4straub d4straub commented Jul 25, 2024 •
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Fix for #767: Reference taxonomy database values were not properly validated in versions 2.9.0 and 2.10.0
Update docs for removed UNITE databases for QIIME2 in #766.

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.
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github-actions bot commented Jul 25, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 0a612fe

+| ✅ 285 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 2.14.1
  • Run at 2024-07-25 11:55:43

erikrikarddaniel
erikrikarddaniel approved these changes Jul 25, 2024
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@erikrikarddaniel erikrikarddaniel left a comment •
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That was quick! :-) Looks all good!
Edit: But now I notice one of the tests fails...

@d4straub
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But now I notice one of the tests fails...

Indeed, I made a mistake with taxlevels, only true was forwarded instead of the actual string, should be fixed now.

@d4straub d4straub merged commit 6549c5b into nf-core:dev Jul 25, 2024
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@d4straub d4straub deleted the fix-ref-taxonomy-validation branch July 25, 2024 12:28
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@erikrikarddaniel erikrikarddaniel erikrikarddaniel approved these changes

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@d4straub @erikrikarddaniel