Add GMM-Demux

[mari-ga]

PR checklist

Closes #XXX

• 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:
  • For modules:
    • nf-core modules test <MODULE> --profile docker
    • nf-core modules test <MODULE> --profile singularity
    • nf-core modules test <MODULE> --profile conda
  • For subworkflows:
    • nf-core subworkflows test <SUBWORKFLOW> --profile docker
    • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
    • nf-core subworkflows test <SUBWORKFLOW> --profile conda

[tstoeriko]

This already looks quite good, great job! I like the input file solution you implemented. I know this module is annoying to implement, so thanks for putting in the work!

There are just two main issues that need addressing:

• inconsistencies regarding file names and input/output patterns
• rather unspecific tests

If anything is unclear don't hesitate to ask.
I've tried to adhere to the review conventions outlined here, I hope it's a helpful format.

[SPPearce]

The tool seems to work fine without specifying any of the optional outputs, can we just test that without the additional config?

[SPPearce]

Currently the prefix is only used in the summary_report_${prefix}.txt file (which should probably be ${prefix}_summary_report.txt).
Do we want to rename the output files with ${prefix}?

[mari-ga]

I added one simple test without nextflow.config, please let me know if it's correct

[SPPearce]

This still has -Stub, and not the actual test output.

[mari-ga]

I ran nf-core modules test gmmdemux --update but didin't create a new snapshot, then deleted the file main.nf.test.snap , but it didn't produce a new file, so I fixed the name from Stub to stub, is that right? I read that it was possible on Slack