adding chewbbaca/createschema module

[anwarMZ]

PR checklist

Closes #4480

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

[anwarMZ]

Thanks to @rpetit3 for his feedback and suggestions

[ggabernet]

It seems like the nf-core lint tests are failing because the meta map is not emitted as output channel. This should be emitted as well, to allow other modules downstream to also use the meta map.

[anwarMZ]

It seems like the nf-core lint tests are failing because the meta map is not emitted as output channel. This should be emitted as well, to allow other modules downstream to also use the meta map.

Thanks for finding that. I have updated the output to emit meta map.

[anwarMZ]

can you kindly add nf-tests for this module docs guidelines

@sateeshperi thank you for your feedback, I have updated the module. This is my first nf-test writing experience, I am running into a failed test. Can you provide some help with this? Thanks

[anwarMZ]

@sateeshperi I updated the stub to create an "n" number of files based on the number of genes and proteins, given that it can be much higher than 20 for bacterial genomes.

I am still failing the test for stub ... looking into it

[SPPearce]

@anwarMZ, do you need some help to finish this PR off?

[SPPearce]

Thanks @JoseEspinosa

[anwarMZ]

Thanks for taking this to the finish line @SPPearce I got pulled into other things in the last little while.

[SPPearce]

No worries @anwarMZ . I swapped the allelecall module to nf-test, but I don't know what it actually wants as input and whether we have it currently available as test data, but we can talk about that on the other PR.