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

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fix/sort-vcf
Feb 12, 2026
Merged

fix: sort final vcf in varlociraptor sbwfs and update varlociraptor#2055
famosab merged 38 commits intodevfrom
fix/sort-vcf

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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 •
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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: 3.5.1.
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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github-actions Bot commented Nov 14, 2025 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 95513ac

+| ✅ 224 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 3.5.1
  • Run at 2026-02-12 17:07:56

@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.

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

Testing now with 2 tumor-normal-pairs

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famosab commented Dec 1, 2025
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Comment thread subworkflows/local/vcf_varlociraptor_somatic/main.nf
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famosab commented Feb 6, 2026

@copilot I always run into this error:

Join mismatch for the following entries: 
  - key=[test3, sample4_vs_sample3, 14, strelka] values= 
  - key=[test3, sample3, 1, strelka] values= 
  - key=[test3, sample4_vs_sample3, 10, strelka] values= 
  - key=[test3, sample3, 3, strelka] values= 
  - key=[test3, sample4_vs_sample3, 12, strelka] values= 
  - key=[test3, sample3, 5, strelka] values= 
  - key=[test3, sample4_vs_sample3, 4, strelka] values= 
  - key=[test3, sample3, 8, strelka] values= 
  - key=[test3, sample4_vs_sample3, 2, strelka] values= 
  - key=[test3, sample4_vs_sample3, 8, strelka] values=
  (more omitted)
  
  
  -[nf-core/sarek] Pipeline completed with errors-
  WARN: Killing running tasks (1)
  ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting
  
   -- Check '/home/runner/tests/4296a60746f9da139b541c5950b714eb/meta/nextflow.log' file for details
  WARN: Failed to render execution report -- see the log file for details
  WARN: Failed to render execution timeline -- see the log file for details
  Nextflow stderr:
  
  



FAILURE: Executed 1 tests in 851.139s (1 failed)

Can you propose changes that fix this issue?

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Copilot AI commented Feb 6, 2026

@famosab I've opened a new pull request, #2125, to work on those changes. Once the pull request is ready, I'll request review from you.

Copilot AI mentioned this pull request Feb 6, 2026
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Copilot AI and others added 5 commits February 6, 2026 12:22
@famosab
Fix join mismatch in varlociraptor somatic workflow for multi-sample …
d08665f 
…processing (#2125)

The varlociraptor somatic subworkflow failed to join normal and tumor
preprocessed BCF files when processing multiple tumor-normal pairs,
causing a "Join mismatch" error.

## Root Cause

The join operation requires matching keys between normal and tumor
channels:
- Normal: `[meta.patient, meta.id, meta.chunk, meta.variantcaller]`
- Tumor: `[meta.patient, meta.normal_id, meta.chunk,
meta.variantcaller]`

After PREPROCESS_NORMAL, `meta.id` was set to the pair ID (e.g.,
"sample4_vs_sample3") instead of the normal sample ID (e.g., "sample3"),
preventing matches with tumor's `meta.normal_id`.

## Changes

**subworkflows/local/vcf_varlociraptor_somatic/main.nf**
- Line 211: Changed normal sample ID assignment from `meta_cram.id` to
`meta_cram.match_id`

```groovy
// Before
meta_vcf + [
    id: meta_cram.id,  // pair ID
    postprocess: 'varlociraptor',
]

// After
meta_vcf + [
    id: meta_cram.match_id,  // normal sample ID
    postprocess: 'varlociraptor',
]
```

This ensures join keys align: normal's `meta.id` now matches tumor's
`meta.normal_id` for each sample pair and chunk.

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---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: famosab <45968370+famosab@users.noreply.github.com>
@famosab
update and change to match_id
a8f8574
@famosab
rm versions
c855936
@famosab
Merge branch 'dev' into fix/sort-vcf
35e8cb8
@famosab
update yte to 1.9.4 and rbt to topics
645e65c
famosab
famosab commented Feb 9, 2026
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@famosab famosab modified the milestone: 3.9.0 Feb 9, 2026
@famosab famosab merged commit b2e39a8 into dev Feb 12, 2026
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@famosab famosab deleted the fix/sort-vcf branch February 12, 2026 17:29
@pinin4fjords pinin4fjords mentioned this pull request May 7, 2026
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

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