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[new module] Add tRNAScan-SE module

Open prototaxites opened this issue 9 months ago • 0 comments

Adds module for tRNAScan-SE.

In local testing, I was having a problem where when running in a Singularity container, the default internal /tmp space would fill up very quickly on large genomes and the program would fail due to lack of disk space. I implemented a solution that moves the working directory from /tmp to the nextflow work dir, but this requires modifying an internal configuration file. Open to better solutions, but this one was working for me.

PR checklist

Closes #XXX

  • [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
  • [ ] If necessary, include test data in your PR.
  • [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:
      • [x] nf-core modules test <MODULE> --profile docker
      • [x] 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

prototaxites avatar Mar 25 '25 12:03 prototaxites