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update to new versions capture for checkm2 databasedownload and checkm2 predict #9744

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update to new versions capture for checkm2 databasedownload and checkm2 predict #9744

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@eit-maxlcummins eit-maxlcummins commented Jan 22, 2026

Updating checkm2 modules to migrate versions to topic channels.

Also fixed a bug with checkm2/databasedownload that causes zenodo to block the user agent model and causes tests to fail. Tests fail even with main branch.

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 module conventions in the contribution docs
  • [-] If necessary, include test data in your PR.
  • [-] Remove all TODO statements.
  • Broadcast software version numbers to topic: versions - See version_topics
  • Follow the naming conventions.
  • [-] Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • [-] Add a resource label
  • [-] Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • For modules:
      • [-] nf-core modules test <MODULE> --profile docker
      • nf-core modules test <MODULE> --profile singularity
      • nf-core modules test <MODULE> --profile conda
    • For subworkflows:
      • nf-core subworkflows test <SUBWORKFLOW> --profile docker
      • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
      • nf-core subworkflows test <SUBWORKFLOW> --profile conda

mashehu
mashehu reviewed Jan 23, 2026
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modules/nf-core/checkm2/databasedownload/tests/main.nf.test
assertAll(
{ assert process.success },
{ assert snapshot(process.out.versions).match() },
{ assert snapshot(process.out.findAll { key, val -> key.startsWith('versions') }).match() },
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@mashehu mashehu Jan 23, 2026

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Any specific reason why process.out.database is not captured?

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