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New module: picard/splitsambynumberofreads

Open Y-Pei opened this issue 6 months ago • 3 comments

PR checklist

Closes #8669

  • [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!
  • [X] If you've added a new tool - have you followed the module conventions in the contribution docs
  • [X] Remove all TODO statements.
  • [X] Emit the versions.yml file.
  • [X] Follow the naming conventions.
  • [X] Follow the parameters requirements.
  • [X] Follow the input/output options guidelines.
  • [X] Add a resource label
  • [X] 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
      • [X] nf-core modules test <MODULE> --profile singularity
      • [x] nf-core modules test <MODULE> --profile conda

Y-Pei avatar Jun 19 '25 15:06 Y-Pei

Also, can the tool work on cram files?

SPPearce avatar Jun 22 '25 10:06 SPPearce

Many thanks for the review and suggestions! All requested changes updated. Re-review please?

Y-Pei avatar Jun 23 '25 15:06 Y-Pei

Does the tool use the fasta index, normally cram files just take the fasta itself

Yes seems like fai is required - would fail without

Y-Pei avatar Jun 30 '25 13:06 Y-Pei

Thank you, I'll stop being nitpicky now ;)

SPPearce avatar Jul 09 '25 18:07 SPPearce