8000 feat: add MuSE as new somatic variant caller by famosab · Pull Request #1744 · nf-core/sarek · GitHub
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Merged
merged 41 commits into from
Mar 12, 2025
Merged

feat: add MuSE as new somatic variant caller #1744

merged 41 commits into from
Mar 12, 2025

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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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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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FriederikeHanssen
FriederikeHanssen reviewed Dec 4, 2024
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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.

@famosab famosab marked this pull request as ready for review February 13, 2025 13:58
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maxulysse
maxulysse reviewed Feb 24, 2025
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maxulysse
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FriederikeHanssen
FriederikeHanssen reviewed Mar 12, 2025
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FriederikeHanssen
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I know this one is closed. @famosab could you please update the metromap, overview image, and readme?

@famosab famosab mentioned this pull request Mar 12, 2025
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famosab added a commit that referenced this pull request Mar 13, 2025
@famosab @FriederikeHanssen @maxulysse
add muse as variant caller to images (#1829)
2465b79 
<!--
# nf-core/sarek pull request

Many thanks for contributing to nf-core/sarek!

Please fill in the appropriate checklist below (delete whatever is not
relevant).
These are the most common things requested on pull requests (PRs).

Remember that PRs should be made against the dev branch, unless you're
preparing a pipeline release.

Learn more about contributing:
[CONTRIBUTING.md](https://github.com/nf-core/sarek/tree/master/.github/CONTRIBUTING.md)
-->

Continues #1744 

## 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](https://github.com/nf-core/sarek/tree/master/.github/CONTRIBUTING.md)
- [ ] If necessary, also make a PR on the nf-core/sarek _branch_ on the
[nf-core/test-datasets](https://github.com/nf-core/test-datasets)
repository.
- [ ] Make sure your code lints (`nf-core pipelines 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).

---------

Co-authored-by: Friederike Hanssen <friederike.hanssen@seqera.io>
Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io>
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen left review comments

@maxulysse maxulysse maxulysse approved these changes

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