8000 srst2/srst2 to nf-test by famosab · Pull Request #8301 · nf-core/modules · GitHub
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Merged
merged 9 commits into from
May 28, 2025
Merged

srst2/srst2 to nf-test #8301

merged 9 commits into from
May 28, 2025

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famosab
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@famosab famosab commented Apr 14, 2025

PR checklist

Closes #7700

  • 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.
  • Emit the versions.yml file.
  • 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 Apr 15, 2025
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Looks like meta.db should probably be a value channel.
The pileup file seems to be unstable too.

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famosab commented May 16, 2025 
│ htsjdk.samtools.SAMException: Sequence name '347__lmr(B)__lmr(B)__00005' doesn't match regex: '[0-9A-Za-z!#$%&+./:;?@^_|~-][0-9A-Za-z!#$%&*+./:;=?@^_|~-]*'                                                                                   │
│ htsjdk.samtools.SAMException: Sequence name '347__lmr(B)__lmr(B)__00005' doesn't match regex: '[0-9A-Za-z!#$%&+./:;?@^_|~-][0-9A-Za-z!#$%&*+./:;=?@^_|~-]*'

@famosab famosab requested a review from jvhagey May 19, 2025 07:52
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famosab commented May 19, 2025

@jvhagey Do you think we can remove the bacteroides fragilis test? Becaus ethat one seems to cause the samtools errors.

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@jvhagey Do you think we can remove the bacteroides fragilis test? Becaus ethat one seems to cause the samtools errors.

I'd say just remove it if we can't figure it out, yes.

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famosab commented May 28, 2025

I decided to comment the tests out for now. There are a couple of instabel things even with the working test data. But for the sake of getting this finished up I would vote for merging this soon. And if the module ever gets updated (unlikely as the tool has not been changed since 2016) this can be tackeld again!

@famosab famosab added this pull request to the merge queue May 28, 2025
Merged via the queue into nf-core:master with commit e16ca6e May 28, 2025
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@famosab famosab deleted the srst branch May 28, 2025 11:09
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@SPPearce SPPearce SPPearce left review comments

@maxulysse maxulysse maxulysse approved these changes

@jvhagey jvhagey Awaiting requested review from jvhagey

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nf-test migration: srst2/srst2
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