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fix: sort final vcf in varlociraptor sbwfs and update varlociraptor #2055

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fix: sort final vcf in varlociraptor sbwfs and update varlociraptor #2055

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@famosab famosab commented Nov 14, 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).

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nf-core-bot commented Nov 14, 2025

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.3.2.
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 Nov 14, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 5d36165

+| ✅ 228 tests passed       |+
#| ❔  13 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 3.3.2
  • Run at 2025-11-26 13:25:38

@famosab famosab changed the title fix: sort final vcf in varlociraptor sbwfs fix: sort final vcf in varlociraptor sbwfs and update varlociraptor Nov 14, 2025
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famosab commented Nov 14, 2025

Needs testing whether this works as expected with multi-sample input.

famosab
famosab commented Nov 18, 2025
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famosab commented Nov 24, 2025

Testing now with 2 tumor-normal-pairs

famosab
famosab commented Dec 1, 2025
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subworkflows/local/vcf_varlociraptor_somatic/main.nf
Comment on lines +231 to +237
ch_normal_for_join = PREPROCESS_NORMAL.out.bcf
.map { meta, normal_bcf -> [[meta.patient, meta.id, meta.chunk, meta.variantcaller], meta, normal_bcf] }
.dump(tag: 'NORMAL_KEY', pretty: true)

ch_tumor_for_join = PREPROCESS_TUMOR.out.bcf
.map { meta, tumor_bcf -> [[meta.patient, meta.normal_id, meta.chunk, meta.variantcaller], meta, tumor_bcf] }
.dump(tag: 'TUMOR_KEY', pretty: true)
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@famosab famosab Dec 1, 2025

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I tried everything here

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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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