Add ComBat-Seq method

[EpigeneMax]

Describe your changes

This PR adds a ComBat-Seq component, based on inmoose implementation.

ComBat-Seq is a state-of-the-art tool for batch correction in bulk RNA-Seq data.
It draws inspiration from ComBat algorithm and adapts it to RNA-Seq.
ComBat is already integrated as a component on this task, adding ComBat-Seq seems quite legitimate.

Checklist before requesting a review

• I have performed a self-review of my code

• Check the correct box. Does this PR contain:

  • Breaking changes
  • New functionality
  • Major changes
  • Minor changes
  • Bug fixes

• Proposed changes are described in the CHANGELOG.md

• CI Tests succeed and look good!

[EpigeneMax]

NB: waiting on approval to run the CI workflow.

[mumichae]

@EpigeneMax Could you update your branch to the latest main commit?

[EpigeneMax]

@EpigeneMax Could you update your branch to the latest main commit?

Done.

[mumichae]

Once it's confirmed that the counts are read correctly, this method can be merged

[rcannood]

Thanks for this! Pushed a few commits rather than leaving a pile of review comments.

The main one: preferred_normalization: counts is right for ComBat-Seq, but the script read X="layers/normalized". The runEach filter hands a counts method the log_cp10k dataset and expects it to pull layers/counts out itself, same as scvi, cellplm and geneformer do. So it was getting log1p CP10K.

pycombat_seq does not complain about that, it just treats the values as counts:

before: layers/normalized    input uniq 5990 range 0.00..    9.1  ->  output uniq  565 range 0.0..   15.0
after:  layers/counts        input uniq  205 range 0.00..12163.0  ->  output uniq  192 range 0.0..12163.0

Rest of that commit:

• adata.X.toarray().T instead of adata.T.to_df().values -- the latter builds a genes x cells DataFrame and copies it twice, ~3 GB at 200k cells
• renamed combat-seq -> combat_seq, the only hyphenated dir under src/methods/
• base image :1.0.0 -> :1, so openproblems is new enough for the component tests in common
• __merge__ to /src/api/comp_method.yaml

Second commit adds it to run_benchmark/main.nf and its dependencies: -- without that it builds and tests but never runs. Drop it if you would rather gate that separately.

viash test src/methods/combat_seq/config.vsh.yaml passes.

[rcannood]

@EpigeneMax Merged main in again and added you to the creditors list. Is orcid 0000-0003-4769-3302 correct?

[rcannood]

Merging -- let me know if anything needs to be updated now that this is merged.