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Fix qiime2 taxonomy part of summary report using unavailable information. #673

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merged 4 commits into from
Dec 12, 2023
Merged

Fix qiime2 taxonomy part of summary report using unavailable information. #673

merged 4 commits into from
Dec 12, 2023

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MatthewJM96
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@MatthewJM96 MatthewJM96 commented Dec 7, 2023 •
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Qiime2 part of the summary report tries to include information from the chosen qiime reference database. In cases where a classifier is used directly, this information may not be available, so I've added to check to see whether it is or not.

PR checklist

  • This comment contains a description of changes (with reason).
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • CHANGELOG.md is updated.

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github-actions bot commented Dec 7, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 04af154

+| ✅ 154 tests passed       |+
#| ❔   3 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 2.10
  • Run at 2023-12-08 14:19:57

d4straub
d4straub approved these changes Dec 8, 2023
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LGTM after you have updated the CHANGELOG ;)

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Update CHANGELOG.md
04af154 
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
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d4straub commented Dec 11, 2023 •
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test_pplace does not produce phyloseq/qiime2_phyloseq.rds any more, I would not have suspected that with the change...

Edit: #676 should fix this!

@d4straub d4straub merged commit 0b29755 into nf-core:dev Dec 12, 2023
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@MatthewJM96 @d4straub