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@mmYeung mmYeung commented Dec 12, 2025

PR checklist

updating input suffix check for reference file input, including nf-tests

Closes #5021

  • [ x ] This comment contains a description of changes (with reason).
  • [ x ] If you've fixed a bug or added code that should be tested, add tests!
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • For modules:
      • [ x ] nf-core modules test <MODULE> --profile singularity

@SPPearce SPPearce enabled auto-merge December 31, 2025 09:03
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SPPearce commented Jan 5, 2026

@mmYeung , if you go to the github-invitations channel on the nf-core slack you can be added to the organisation, then the tests will run automatically.

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mmYeung commented Jan 6, 2026

Thanks @SPPearce, I've submitted a request on the Slack channel.

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SPPearce commented Jan 6, 2026

So one of the new files being generated is empty, which means that you have to explicitly change the nf-test assertion to only check for existence (else it is easy to accidentally assume the tool has worked properly when it is actually making empty files)

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Verifybamid2 does not allow for reference files ending with '.fa'

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