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Merge intervals for WES in GATK GenomicsDBImport #1777

Merged
merged 3 commits into from
Jan 27, 2025
Merged

Merge intervals for WES in GATK GenomicsDBImport #1777

merged 3 commits into from
Jan 27, 2025

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tdanhorn
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@tdanhorn tdanhorn commented Jan 23, 2025 •
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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 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).

Running sarek with --joint_germline on WES samples with an intervals file containing many thousands of targets causes GATK GenomicsDBImport to create millions of files and run for several days without completing. Adding the --merge-intervals option to that process fixes that. This PR add the parameter conditional on the --wes pipeline parameter.

Closes #1776

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github-actions bot commented Jan 23, 2025 •
edited by nf-core-bot
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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.

@tdanhorn tdanhorn changed the base branch from master to dev January 23, 2025 00:16
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github-actions bot commented Jan 23, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 9868622

+| ✅ 215 tests passed       |+
#| ❔  11 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ 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!

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2025-01-27 13:43:09

FriederikeHanssen
FriederikeHanssen previously approved these changes Jan 27, 2025
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LGTM! Thank you!

@maxulysse maxulysse merged commit dfb2d15 into dev Jan 27, 2025
38 checks passed
@FriederikeHanssen FriederikeHanssen deleted the genomicsdbimport-merge-intervals branch January 27, 2025 18:18
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@maxulysse maxulysse maxulysse approved these changes

@FriederikeHanssen FriederikeHanssen FriederikeHanssen left review comments

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Joint germline: GATK GenomicsDBImport chokes on millions of files with WES intervals file
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@tdanhorn @maxulysse @FriederikeHanssen