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Update vcf_annotate_snpeff subworkflow#2141

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famosab wants to merge 4 commits intodevfrom
update/vcf_annotate_snpeff
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Update vcf_annotate_snpeff subworkflow#2141
famosab wants to merge 4 commits intodevfrom
update/vcf_annotate_snpeff

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@famosab
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@famosab famosab commented Feb 13, 2026

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 Feb 13, 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.

@famosab famosab mentioned this pull request Feb 13, 2026
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github-actions bot commented Feb 13, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 07758e4

+| ✅ 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 2026-02-13 13:19:16

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maxulysse commented Feb 13, 2026

the snpeff and ensemblvep reports now have 4 item in the channels instead of 2

maxulysse
maxulysse reviewed Feb 13, 2026
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@FriederikeHanssen FriederikeHanssen Awaiting requested review from FriederikeHanssen FriederikeHanssen is a code owner

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