Umitools prepare for rsem

[emmarousseau]

Description

Add prepare-for-rsem UMItools component

Checklist before requesting a review

• I have performed a self-review of my code

• Conforms to the Contributing guidelines

• Proposed changes are described in the CHANGELOG.md

• I have tested my code with viash ns test --parallel -q <name or namespace>

• Check the correct box. Does this PR contain:

  • Breaking changes
  • New functionality
  • Major changes
  • Minor changes
  • Documentation
  • Bug fixes

[tverbeiren]

Please see code comments.

[tverbeiren]

The Python script has an undocumented argument for retrieving the version:

    parser = U.OptionParser(version="%prog version: $Id$", usage=usage, description=globals()["__doc__"])

I suggest you use that for version instead of the pip dependencies.

[tverbeiren]

The name of the component is different in the CHANGELOG and the config.vsh.yaml, please align.

[tverbeiren]

One more thing: please move the samtools installation in the test.sh script to the beginning of the test script so the output does not interfere with the output of the tests themselves.

[emmarousseau]

Nirmayi pointed out the you can use the prepare-for-rsem command directly instead of calling the python script, but the version argument for that tools specifically does not work (at least for me, output below), so I included the general umi_tools version.

umi_tools prepare-for-rsem --version 
# prepare-for-rsem version: $Id$