feat: addition of vembrane sort module

[mkatsanto]

PR checklist

Fixes #9265

Addition of the vembrane sort module https://github.com/vembrane/vembrane

• [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] 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
    • [ ] nf-core modules test <MODULE> --profile singularity
    • [X] nf-core modules test <MODULE> --profile conda

[famosab]

vembrane sort: error: argument --output-fmt/-O: invalid choice: 'vcf.gz' (choose from vcf, bcf, uncompressed-bcf)

[famosab]

Seems like gzipped vcfs are not allowed. I would suggest to open an issue over at the vembrane repo to request that and remove it from the module for now :) You can link to the PR in the issue you open :)

[famosab]

@mkatsanto do you have time to finish this? :) then I would give it another round of review - or do you need some help / me to pick it up (both would be fine!)

[mkatsanto]

@mkatsanto do you have time to finish this? :) then I would give it another round of review - or do you need some help / me to pick it up (both would be fine!)

@famosab I can do this tomorrow, but if you are in a hurry please go ahead!

[famosab]

No, no hurry at all :) I was just wondering because we never talked about it during the Hackathon! Thank you!!!

[famosab]

Opened the issue here: https://github.com/vembrane/vembrane/issues/231

[famosab]

@mkatsanto can you run pre-commit run --all-files locally and push that to the branch? :) then we should be good to go