Umitools prepareforrsem

[pinin4fjords]

Adding UMI tools' prepare for rsem script. This will be a native command in the next release of UMI tools, but for now I'm bundling the python with the module as a template.

See:

• Problems with dedup output and RSEM CGATOxford/UMI-tools#465
• {is} prepare for rsem CGATOxford/UMI-tools#609

PR checklist

• 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:
  • 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

[maxulysse]

Almost perfect

[pinin4fjords]

Thanks @maxulysse !