4457 new module chewbaccaallelecall

[anwarMZ]

PR checklist

Closes #4457

• [ ] This comment contains a description of changes (with reason).
• [ ] 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
• [ ] If necessary, include test data in your PR.
• [x] Remove all TODO statements.
• [x] Emit the versions.yml file.
• [x] Follow the naming conventions.
• [ ] Follow the parameters requirements.
• [x] Follow the input/output options guidelines.
• [ ] 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:
  • [ ] 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

[anwarMZ]

This is a draft PR, this module requires a schema to run which is currently not in test-datasets. A sister module is currently in development - #4480 which generates the schema. That will be added to tests/modules/nf-core/chewbbaca/allelecall/main.nf

[SPPearce]

Hi @anwarMZ, Are you still interested in getting this module merged in? It will need converting to the more recent specifications that are being used in the modules repo, which may include:

• using nf-test instead of pytest
• conda definition in a environment.yml file separate from the main.nf
• adding a stub
• updating the meta.yml file to reflect the latest specification (better reflecting the channel output rather than a flat list)

If you need help we can provide that, but if you aren't going to work on it in the near future then we will close this PR next week (it can be reopened in the future if someone wants to work on it again).

[anwarMZ]

Hi @SPPearce, thanks for the reminder. Yes, I will update this PR soon and ask for quick help where needed.

[anwarMZ]

@SPPearce I have updated the module, please let me know if you have any concerns.

[anwarMZ]

@SPPearce updated accordingly. Thank you for the feedback

[anwarMZ]

Thanks. Almost there I think. Just noticed that some of your output channels are optional, but you are using mv to rename the files - this will fail and error if the file isn't generated I think. You can wrap it in an existence check or maybe use an argument for mv, not sure (and reviewing on my phone)

updated with 6ec7e03