Add formula based contrasts to `deseq2`

[atrigila]

https://github.com/nf-core/differentialabundance/issues/459

Draft POC / work in progress

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.
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• [ ] 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

[atrigila]

I am not sure why only the conda test is failing even after setting seed.

Any ideas how to move forward? cc @grst @pinin4fjords

[pinin4fjords]

It's probably just floating point differences (IIRC there are rounding controls somewhere to help).

If you can, run with Docker and conda and compare the files to be sure.

[atrigila]

Since I made changes to the module and the subworkflow abundance_differential_filter, CI tests now also trigger differential_functional_enrichment. However, I did not make any changes that could affect that subworkflow and the failing tests are not related to the changes made in this PR. It seems like they are related to the tests involving 'gprofiler2'. Since the module gprofiler2 uses a URL in its call, I suspect that there might have been changes in that website.

[atrigila]

Could I get your review @pinin4fjords? Thank you!

[atrigila]

I addressed the additional comments, and I am going to merge this PR to be able to continue in differentialabundance. If you later see any further changes that need to be addressed, please let me know.

[atrigila]

I need @grst's approval, as he requested changes, but he is currently OOO.