New module: SoupX ambient RNA removal

[LeonHafner]

PR checklist

• [x] 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.
• [ ] Remove all TODO statements.
• [x] Emit the versions.yml file.
• [x] Follow the naming conventions.
• [ ] Follow the parameters requirements.
• [ ] 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:
  • For modules:
    • [ ] nf-core modules test <MODULE> --profile docker
    • [ ] nf-core modules test <MODULE> --profile singularity
    • [ ] nf-core modules test <MODULE> --profile conda

[LeonHafner]

@nf-core-bot fix linting

[github-actions[bot]]

Nothing for me to do here! :shrug: This is probably because the linting errors come from nf-core lint and have to be fixed manually (or with nf-core lint --fix).

[nictru]

Should switch this to an R implementation. This Vignette can serve as a template. Should use AnndataR if the file ends with .h5ad otherwise readRDS.

[LeonHafner]

@nictru what's the plan with this PR? AnnDataR isn’t available on bioconda yet, as it hasn’t had its first release.

[famosab]

@LeonHafner @nictru Are you still working on this PR?

[LeonHafner]

New information about anndataR and when it will be added to bioconda: https://github.com/scverse/anndataR/issues/254#issuecomment-2731847030