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feat: add MuSE as new somatic variant caller #1744

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feat: add MuSE as new somatic variant caller #1744

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famosab
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@famosab famosab commented Dec 4, 2024 •
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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/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).

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github-actions bot commented Dec 4, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 59dde7b

+| ✅ 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 2024-12-05 15:58:03

maxulysse
maxulysse reviewed Dec 4, 2024
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maxulysse
maxulysse reviewed Dec 4, 2024
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@famosab famosab linked an issue Dec 4, 2024 that may be closed by this pull request
new variant caller: MuSE #1742
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FriederikeHanssen
FriederikeHanssen reviewed Dec 4, 2024
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subworkflows/local/bam_variant_calling_somatic_muse/main.nf Outdated
Comment on lines 23 to 33
CRAM_TO_BAM_TUMOR(
cram.map{ meta, normal_cram, normal_crai,tumor_cram, tumor_crai -> [ meta + [ tobam: 'tumor' ], tumor_cram, tumor_crai ] },
fasta,
fai
)

CRAM_TO_BAM_NORMAL(
cram.map{ meta, normal_cram, normal_crai,tumor_cram, tumor_crai -> [ meta + [ tobam: 'normal' ], normal_cram, normal_crai ] },
fasta,
fai
)
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we should think of a more general strategy, we now have a couple of tools that require BAM files instead. if someone would run cnvkit and muse right now they would do the conversion twice which is wasteful

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I suppose there is no way the muse dev would add cram support?

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I can ask the team for sure but I would not wait for them with this PR. I can try and do the conversion for both cnvkit and muse -> are there any other tools that also need this?

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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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@FriederikeHanssen FriederikeHanssen FriederikeHanssen left review comments

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new variant caller: MuSE
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@famosab @nf-core-bot @maxulysse @FriederikeHanssen