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Add splice junctions input to STAR align

Open cguyomar opened this issue 3 years ago • 0 comments

This PR adds splice junction files as an input for STAR align. This is necessary to perform 2 pass mapping (See STAR manual section 8.1), and useful for RNAseq variant calling (could be used in nf-core/rnavar I guess). I also added a small test case. The PR for the test data needs to be merged for it to work though. This is my first PR on nf-core, many thanks with your help :)

PR checklist

  • [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 necessary, include test data in your PR.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • [X] PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
    • [X] PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
    • [X] PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware

cguyomar avatar Aug 04 '22 10:08 cguyomar