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Fix bcftools concat on Strelka somatic VCFs#2128

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FriederikeHanssen merged 4 commits intodevfrom
fix/strelka-concat-allow-overlaps
Feb 11, 2026
Merged

Fix bcftools concat on Strelka somatic VCFs#2128
FriederikeHanssen merged 4 commits intodevfrom
fix/strelka-concat-allow-overlaps

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@FriederikeHanssen FriederikeHanssen commented Feb 8, 2026

Summary

  • Strelka somatic produces separate SNV and INDEL VCFs, both covering all chromosomes. When bcftools concat merges them during consensus calling, it fails with "chromosome block chr1 is not contiguous" because the same chromosomes appear in both files.
  • Adds --allow-overlaps to the BCFTOOLS_CONCAT args in the consensus subworkflow config, which performs a merge-sort of the inputs and produces correctly ordered output.
  • Moves Fix regex patterns for dbnsfp_tbi and spliceai parameters #2113 changelog entry from 3.7.1 to 3.8.0 where it belongs.

Test plan

  • Run full-size somatic test with Strelka + consensus calling enabled
  • Verify concatenated VCF is properly sorted and indexed

🤖 Generated with Claude Code

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nf-core-bot commented Feb 8, 2026

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 Feb 8, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 749f918

+| ✅ 223 tests passed       |+
#| ❔  13 tests were ignored |#
!| ❗   8 tests had warnings |!
Details

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 3.8.1
  • 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 2026-02-11 09:52:01

@FriederikeHanssen @claude
Fix bcftools concat failing on Strelka somatic VCFs with non-contiguo…
79c8b96 
…us chromosomes

Strelka somatic outputs separate SNV and INDEL VCFs, both covering all
chromosomes. bcftools concat without --allow-overlaps fails because
chromosome blocks are non-contiguous across the two files.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
@FriederikeHanssen FriederikeHanssen force-pushed the fix/strelka-concat-allow-overlaps branch from 6f25df6 to 79c8b96 Compare February 8, 2026 22:42
maxulysse
maxulysse approved these changes Feb 8, 2026
View reviewed changes
Comment thread CHANGELOG.md

### Fixed

- [#2050](https://github.com/nf-core/sarek/issues/2050) - Fix regex patterns for `dbnsfp_tbi`, `spliceai_snv`, and `spliceai_snv_tbi` parameter validation
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@maxulysse maxulysse Feb 8, 2026

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Why removing this from changelog?

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@FriederikeHanssen FriederikeHanssen Feb 9, 2026

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It was in the wrong section (for 3.6.1) moved it up to this release

@FriederikeHanssen FriederikeHanssen merged commit 076faad into dev Feb 11, 2026
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@maxulysse maxulysse maxulysse approved these changes

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