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Export all process software versions #719

Merged
merged 4 commits into from
Mar 26, 2024
Merged

Export all process software versions #719

merged 4 commits into from
Mar 26, 2024

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d4straub
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@d4straub d4straub commented Mar 26, 2024 •
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Until now only software versions of selected processes were listed, this is changed here so that software versions of all processes are now exported to pipeline_info/software_versions.yml.

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>).
  • 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).

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github-actions bot commented Mar 26, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 0297f1a

+| ✅ 191 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 2.13.1
  • Run at 2024-03-26 15:01:32

@d4straub d4straub added this to the 2.9.0 milestone Mar 26, 2024
erikrikarddaniel
erikrikarddaniel approved these changes Mar 26, 2024
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Looks good, except for some missing END_VERSIONS -- maybe it works anyway?

modules/local/format_taxonomy.nf Show resolved Hide resolved
@d4straub d4straub merged commit 0c24ff3 into nf-core:dev Mar 26, 2024
17 checks passed
@d4straub d4straub deleted the export-all-versions branch March 26, 2024 15:34
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@erikrikarddaniel erikrikarddaniel erikrikarddaniel approved these changes

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