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POC immunedeconv as functional method and fix error for custom column#656

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delfiterradas wants to merge 1 commit intonf-core:devfrom
delfiterradas:immunedeconv
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POC immunedeconv as functional method and fix error for custom column#656
delfiterradas wants to merge 1 commit intonf-core:devfrom
delfiterradas:immunedeconv

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@delfiterradas delfiterradas commented Mar 5, 2026

This is a POC to make immunedeconv a functional method (#469) and also add automatic detection and conversion of ENSEMBL gene IDs (human/mouse) to gene symbols, with safe fallback to the first column if gene_symbol_col is missing (#512).

PR checklist

  • 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 pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/differentialabundance branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nf-test test main.nf.test -profile test,docker).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@delfiterradas delfiterradas self-assigned this Mar 5, 2026
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