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Merged
FriederikeHanssen merged 34 commits into from
Apr 24, 2025
Merged

Add bcftools normalization #1770

FriederikeHanssen merged 34 commits into from
Apr 24, 2025

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@maxulysse
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@maxulysse maxulysse commented Jan 13, 2025 •
edited by tdanhorn
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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).

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 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).

@Patricie34 @JC-Delmas
@maxulysse @FriederikeHanssen
Sarek bcftools normalization (#1682)
33b0ba6 
<!--
# 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)
-->

## PR checklist

- [x] This comment contains a description of changes (with reason).
- [ ] If you've fixed a bug or added code that should be tested, add
tests!
- [x] 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 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.
- [x] Output Documentation in `docs/output.md` is updated.
- [x] `CHANGELOG.md` is updated.
- [x] `README.md` is updated (including new tool citations and
authors/contributors).

---------

Co-authored-by: JC-Delmas <delmas.jeancharles@yahoo.fr>
Co-authored-by: Jean-Charles Delmas <130393309+JC-Delmas@users.noreply.github.com>
Co-authored-by: Maxime U Garcia <maxime.garcia@seqera.io>
Co-authored-by: Friederike Hanssen <friederike.hanssen@seqera.io>
Co-authored-by: Maxime U Garcia <max.u.garcia@gmail.com>
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nf-core-bot commented Jan 13, 2025

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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github-actions bot commented Jan 13, 2025 •
edited
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 9d9ffc3

+| ✅ 214 tests passed       |+
#| ❔  12 tests were ignored |#
!| ❗   7 tests had warnings |!
Details

❗ Test warnings:

  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • 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!
  • schema_lint - Input mimetype is missing or empty
  • schema_description - No description provided in schema for parameter: markduplicates_pixel_distance
  • schema_description - No description provided in schema for parameter: gatk_pcr_indel_model

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2025-04-24 12:17:48

@maxulysse
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maxulysse commented Feb 25, 2025

@Patricie34 I synced dev with this branch that now includes the updates from #1806

@maxulysse maxulysse mentioned this pull request Mar 3, 2025
Merged
11 tasks
@maxulysse
add tests for normalization and concat + normalize (#1815)
1831c68 
<!--
# 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)
-->

## 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).
maxulysse
maxulysse commented Mar 4, 2025
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@maxulysse maxulysse changed the title Finally merge in Sarek bcftools normalization (#1682) Add bcftools normalization Mar 4, 2025
maxulysse
maxulysse commented Mar 4, 2025
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maxulysse
maxulysse commented Mar 4, 2025
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maxulysse
maxulysse commented Apr 9, 2025
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maxulysse
maxulysse commented Apr 9, 2025
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FriederikeHanssen
FriederikeHanssen requested changes Apr 15, 2025
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maxulysse
maxulysse commented Apr 16, 2025
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@FriederikeHanssen FriederikeHanssen merged commit c960ab3 into dev Apr 24, 2025
25 checks passed
@maxulysse maxulysse deleted the dev_normalization branch April 25, 2025 07:58
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@maxulysse @nf-core-bot @FriederikeHanssen @Patricie34