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New module: SoupX ambient RNA removal #6879

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@LeonHafner LeonHafner commented Oct 28, 2024 •
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PR checklist

  • 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

@LeonHafner LeonHafner added new module Adding a new module draft labels Oct 28, 2024
@LeonHafner
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@nf-core-bot fix linting

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Nothing for me to do here! 🤷
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
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nictru commented Oct 30, 2024

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 LeonHafner linked an issue Nov 1, 2024 that may be closed by this pull request
Create nf-core module for SoupX nf-core/scdownstream#112
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@LeonHafner
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@nictru what's the plan with this PR? AnnDataR isn’t available on bioconda yet, as it hasn’t had its first release.

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famosab commented Mar 11, 2025

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

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New information about anndataR and when it will be added to bioconda: scverse/anndataR#254 (comment)

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Create nf-core module for SoupX
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@LeonHafner @nictru @famosab