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Support for PureCN #1710

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Support for PureCN #1710

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@lbeltrame lbeltrame commented Oct 29, 2024 •
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This PR implements support for PureCN (https://github.com/lima1/).

Design rationale talked at the hackathon:

  • Assume a PoN has been made already ("NormalDB", in PureCN-speak)
  • Don't calculate coverage from PureCN, use GATK4, which supports CRAM input (however denoising requires a PoN, so this makes things a little more complicated)
  • Use an interval file already processed by PureCN (done in Sarek first)

CI is failing, but in areas I didn't touch (hopefully!)

TODO:

  • Tests
  • Docs
  • Actually testing this with real data

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/sarek branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • 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).

@lbeltrame lbeltrame self-assigned this Oct 29, 2024
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github-actions bot commented Oct 29, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 82d477e

+| ✅ 215 tests passed       |+
#| ❔  11 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 2024-10-30 10:08:43

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lbeltrame commented Oct 29, 2024 •
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@FriederikeHanssen @maxulysse

I didn't hook the VCF part yet, because PureCN depends on MuTect2, but it also requires specific parameters:

Make sure to run Mutect 2 with --genotype-germline-sites true --genotype-pon-sites true. You will not get usuable output without those flags. Since Mutect 2 from GATK 4.2.0+, average base quality scores can be very low and variants will be too aggressively removed by PureCN. You will need to set --min-base-quality 20 in PureCN.R to keep them.

(https://www.bioconductor.org/packages/devel/bioc/vignettes/PureCN/inst/doc/Quick.html#3_Create_VCF_files)

What can we do in this case? Discussed in person, assume that:

a. MuTect2 is being run;
b. MuTect2 was run with the right parameters (how to warn if not?)

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lbeltrame commented Oct 29, 2024 •
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Also lint fails, what's the recommended way to patch those modules to make sure nf-core lint is happy? Should be fixed with patches.

@lbeltrame
Fix linting (hopefully) by doing patches
d956a4c
@lbeltrame
A little change to the PureCN module
6b666fe 
This needs to be upstreamed pronto!
@lbeltrame
Update patch
5531eca
@lbeltrame
Require a MuTect2 VCF for PureCN
9e713bb 
As discussed as the hackathon, we can reasonably assume PureCN is
run in the recommended way.
@lbeltrame
Enable PureCN with tumor-only Mutect too
82d477e 
As long as Mutect has been run with a PoN, PureCN can work with it.
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From the implementation side, at least conceptually, everything should be in place. I can't test this here at the hackathon, so this will have to wait until I'm back to use some real-world tests.

@lbeltrame lbeltrame changed the title Support for PureCN (do not merge, early draft) Support for PureCN Oct 30, 2024
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@FriederikeHanssen FriederikeHanssen Awaiting requested review from FriederikeHanssen FriederikeHanssen will be requested when the pull request is marked ready for review FriederikeHanssen is a code owner

@maxulysse maxulysse Awaiting requested review from maxulysse maxulysse will be requested when the pull request is marked ready for review maxulysse is a code owner

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