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Remove Strelka tumor-only somatic variant calling #1709

Merged
merged 5 commits into from
Oct 29, 2024
Merged

Remove Strelka tumor-only somatic variant calling #1709

merged 5 commits into from
Oct 29, 2024

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nevinwu
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@nevinwu nevinwu commented Oct 29, 2024 •
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Closes #803.

I have removed strelka tumor-only somatic variant calling from the bam_variant_calling_tumor_only_all subworkflow. Also i have updated the subway image, docs and tests.

Maybe we should leave the PR open for a few days to see if anyone complains about removing it: https://nfcore.slack.com/archives/CGFUX04HZ/p1730110553053079

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 Oct 29, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e474240

+| ✅ 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 2024-10-29 10:28:47

@maxulysse
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issue with controlfreec test

@maxulysse
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Seems to be a random issue, so I'll retrigger

@maxulysse maxulysse merged commit 1ba8cee into nf-core:dev Oct 29, 2024
53 of 57 checks passed
@nevinwu nevinwu deleted the dev branch October 29, 2024 11:48
@FriederikeHanssen
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@rannick tagging you so we don't forget. We can easily revert this PR, if this feature is critical to you :)

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@FriederikeHanssen FriederikeHanssen Awaiting requested review from FriederikeHanssen FriederikeHanssen is a code owner

@maxulysse maxulysse Awaiting requested review from maxulysse maxulysse is a code owner

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@nevinwu @maxulysse @FriederikeHanssen