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add modules for sra-human-scrubber

Open rpetit3 opened this issue 3 years ago • 1 comments

PR checklist

Closes https://github.com/nf-core/modules/issues/2693

  • [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] 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:
    • [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

SRA Human Scrubber uses a >1gb database, so I went with stub runs for the tests.

rpetit3 avatar Dec 23 '22 22:12 rpetit3

@rpetit3 , it looks like the version naming structure for the database has changed: https://ftp.ncbi.nlm.nih.gov/sra/dbs/human_filter/README.txt

SPPearce avatar May 09 '24 10:05 SPPearce

@rpetit3 Do you still plan to finish this module?

famosab avatar Mar 10 '25 15:03 famosab