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strict syntax + versions topic #9693

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strict syntax + versions topic #9693

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@vagkaratzas vagkaratzas commented Jan 19, 2026 •
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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

SPPearce
SPPearce reviewed Jan 19, 2026
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modules/nf-core/hhsuite/reformat/main.nf Outdated
output:
tuple val(meta), path("${prefix}.${outformat}.gz"), emit: msa
path "versions.yml" , emit: versions
tuple val("${task.process}"), val("hhsuite"), eval('hhblits -h | grep \'HHblits\' | sed -n -e \'s/.*\\([0-9]\\+\\.[0-9]\\+\\.[0-9]\\+\\).*/\\1/p\''), topic: versions, emit: versions_hhsuite
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@SPPearce SPPearce Jan 19, 2026

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I'm sure this command could be simplified, maybe with some help from AI.

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@vagkaratzas vagkaratzas Jan 19, 2026

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Done

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@SPPearce SPPearce SPPearce approved these changes

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@vagkaratzas @SPPearce