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Port sentieon bwaindex to nf-test #6999

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PR checklist

Closes #XXX

  • 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

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Presumably this PR is not complete?
pytest files are still present, no stub test.

@@ -0,0 +1,9 @@
env {
// NOTE This is how nf-core/sarek users will use Sentieon in real world use
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Suggested change
// NOTE This is how nf-core/sarek users will use Sentieon in real world use
// NOTE This is how nf-core/sarek users will use Sentieon in real world use

Not all the world is sarek ;)

@SPPearce SPPearce marked this pull request as draft November 20, 2024 15:13
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