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Fix: Update variant calling tool - data type table in docs #1635

Merged
merged 10 commits into from
Dec 10, 2024
Merged

Fix: Update variant calling tool - data type table in docs #1635

merged 10 commits into from
Dec 10, 2024

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famosab
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@famosab famosab commented Aug 28, 2024 •
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PR checklist

Closes #803

  • 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).

I updated Normal -> Germline, Tumor -> Tumow-Only, Somatic -> Somatic (Tumor-Normal) to clarify the docs. I changed Strelka to not being able to process tumor-only samples and MSI to being able to process tumor-only.

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github-actions bot commented Aug 28, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit ed95c83

+| ✅ 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 2024-12-10 10:00:13

@bounlu
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bounlu commented Aug 28, 2024

In the current pipeline, MSIsensorpro doesn't work with tumor-only samples, unless you merge my PR.

@famosab famosab linked an issue Aug 29, 2024 that may be closed by this pull request
Can be tumor-only somatic variant calling performed using Strelka? #803
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@famosab famosab changed the title Update variant calling tool - data type table in docs Fix: Update variant calling tool - data type table in docs Sep 3, 2024
maxulysse
maxulysse previously approved these changes Oct 4, 2024
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maxulysse
maxulysse reviewed Oct 4, 2024
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@FriederikeHanssen @maxulysse
Update docs/usage.md
1ccf16b 
Co-authored-by: Maxime U Garcia <[email protected]>
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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: 2.14.1.
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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@nf-core-bot fix linting

FriederikeHanssen
FriederikeHanssen reviewed Dec 10, 2024
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@FriederikeHanssen FriederikeHanssen merged commit fb5bdbf into nf-core:dev Dec 10, 2024
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

@maxulysse maxulysse maxulysse approved these changes

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Can be tumor-only somatic variant calling performed using Strelka?
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@famosab @bounlu @nf-core-bot @FriederikeHanssen @maxulysse