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Lint modules for missing self.add_software_version #2081

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merged 10 commits into from
Sep 28, 2023

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pontushojer
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@pontushojer pontushojer commented Sep 27, 2023

Related to #2042

  • Adds new code check for making sure each module/submodule calls self.add_software_version.
  • Updated docs so that developers of new modules/submodules are aware that they need to include a self.add_software_version call
  • For modules missing software version a superfluous self.add_software_version calls are added.
  • Adds version parsing for remaining modules (see Software Versions: Add support to all modules #2051):
    • seqyclean
    • sexdetermine
    • skewer
    • slamdunk
    • snippy
    • snpeff
    • snpsplit
    • umitools
    • vep

For some modules I could find version information in the logs but in files that are currently unparsed e.g. dragen, or is missing from the current testdata e.g. fastp . I will raise separate issues for these.

  • This comment contains a description of changes (with reason)
  • CHANGELOG.md has been updated

@vladsavelyev
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Really-really love it! Thanks so much for the superfluous lines and for the CI check 🙏

@vladsavelyev vladsavelyev changed the title Check for modules missing version parsing Lint modules for missing self.add_software_version Sep 28, 2023
@vladsavelyev
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@multiqc-bot changelog

@vladsavelyev vladsavelyev merged commit db43f62 into MultiQC:master Sep 28, 2023
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a-frantz added a commit to a-frantz/MultiQC that referenced this pull request Oct 2, 2023
* master:
  Just run CI on the oldest + newest supported Python versions (MultiQC#2074)
  Picard: fix parsing mixed strings/numbers, account for trailing tab (MultiQC#2083)
  FastQC: add top overrepresented sequences table (MultiQC#2075)
  Add GitHub Actions bot workflow to fix code linting from a PR comment (MultiQC#2082)
  Use custom exception type instead of `UserWarning` when no samples are found. (MultiQC#2049)
  Lint modules for missing `self.add_software_version` (MultiQC#2081)
  Changelog bot: Update docs (MultiQC#2077)
  Changelog action: remove `.capitalize()`, add changelog entry (MultiQC#2080)
  Add action to populate the change log from PR titles triggered by `@multiqc-bot changelog` (MultiQC#2025)

# Conflicts:
#	CHANGELOG.md
#	multiqc/modules/ngsderive/ngsderive.py
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3 participants