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Add immunedeconv module #421

Merged
merged 2 commits into from
Jan 22, 2025
Merged

Add immunedeconv module #421

merged 2 commits into from
Jan 22, 2025

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nschcolnicov
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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).

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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.0.2.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

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github-actions bot commented Jan 15, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 79c7a08

+| ✅ 304 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2025-01-21 21:06:48

@nschcolnicov nschcolnicov mentioned this pull request Jan 15, 2025
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@nschcolnicov nschcolnicov marked this pull request as ready for review January 15, 2025 21:09
@pinin4fjords
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sorry, I'm not familiar with immunedeconv. Could you please update the description to describe the module and how it fits into the overall themes of the workflow? The name makes it sound like something quite specialist.

@grst
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grst commented Jan 16, 2025

Hi @pinin4fjords, see also the corresponding issue here:
#361

Cell-type deconvolution is common downstream analysis step for RNA-seq data to estimate (immune) cell-type fractions and compare them between conditions. It would be one of several methods for "functional analyses" that we think this workflow could benefit from: #367

The one thing I'd like to see in addition to what's done in this PR is to include the results in some sort of report. But this can (and probably should) be addressed separately.

@pinin4fjords
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OK, looking pretty good. I assume all the signatures are 'baked in' to this method- does there need to be any provision for a custom matrix to supply those?

@nschcolnicov nschcolnicov mentioned this pull request Jan 17, 2025
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@nschcolnicov
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OK, looking pretty good. I assume all the signatures are 'baked in' to this method- does there need to be any provision for a custom matrix to supply those?

Hi @pinin4fjords as far as I understand the tool, this is currently not possible: https://omnideconv.org/immunedeconv/articles/immunedeconv.html#can-i-specify-a-custom-signature-matrix-through-immunedeconv, maybe @grst can confirm.

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grst commented Jan 20, 2025

immundeconv supports custom matrices for some tools, but that's more of a niche use-case. It's really intended to be ran with the predefined signature that are shipped with the methods.

Having predefined signatures makes it really convenient to use. There's a lot of other methods that support custom signature matrices (typically derived from scRNA-seq data) that we collected in omnideconv.
Supporting such tools could be interesting, too, but that would be a separate module.

pinin4fjords
pinin4fjords requested changes Jan 20, 2025
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OK, gotcha.

I'm sorry, I hate to make you do it (mostly because I hate doing it), but I think you're going to have to update the metro map before this gets merged.

@nschcolnicov nschcolnicov merged commit 6ecc48c into dev Jan 22, 2025
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@pinin4fjords pinin4fjords pinin4fjords approved these changes

@grst grst Awaiting requested review from grst

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@nschcolnicov @nf-core-bot @pinin4fjords @grst