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New module: tiledbvcf

Open atrigila opened this issue 2 years ago • 7 comments

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
  • [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
  • [ ] 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:
    • [ ] PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
    • [ ] PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware
    • [ ] PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware

Two modules: TileDB VCF create and TileDB VCF store. Pending tasks:

  • [ ] handle absence of singularity container and bioconda recipe
  • [ ] handle "- Empty file found!" when running tests in tiledbvcf_create. This is the expected behaviour as we are creating an empty datastore.

atrigila avatar Feb 03 '23 15:02 atrigila