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Add VEP Phenotypes plugin support#2094

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FriederikeHanssen merged 3 commits intodevfrom
vep-plugin-phenotypes
Jan 13, 2026
Merged

Add VEP Phenotypes plugin support#2094
FriederikeHanssen merged 3 commits intodevfrom
vep-plugin-phenotypes

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@FriederikeHanssen FriederikeHanssen commented Jan 12, 2026

Add support for the VEP Phenotypes plugin which retrieves overlapping phenotype information from Ensembl's phenotype annotation databases. The plugin maps phenotype data to genomic features including genes, variants, and QTLs.

Parameters:

  • --vep_phenotypes: Enable the plugin
  • --phenotypes_file: Optional path to phenotype GFF/GVF file (auto-downloads if not specified)
  • --phenotypes_include_types: Optional filter for feature types (Gene, Variation, QTL, StructuralVariation)

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).

@FriederikeHanssen @claude
Add VEP Phenotypes plugin support
c7c7d84 
Add support for the VEP Phenotypes plugin which retrieves overlapping phenotype information from Ensembl's phenotype annotation databases. The plugin maps phenotype data to genomic features including genes, variants, and QTLs.

Parameters:
- --vep_phenotypes: Enable the plugin
- --phenotypes_file: Optional path to phenotype GFF/GVF file (auto-downloads if not specified)
- --phenotypes_include_types: Optional filter for feature types (Gene, Variation, QTL, StructuralVariation)

Co-Authored-By: Claude Sonnet 4.5 <[email protected]>
FriederikeHanssen
FriederikeHanssen commented Jan 12, 2026
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github-actions bot commented Jan 12, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 4bb243f

+| ✅ 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 2026-01-13 09:43:37

Base automatically changed from vep-plugin-mastermind to dev January 13, 2026 09:23
@FriederikeHanssen FriederikeHanssen merged commit 2fd3831 into dev Jan 13, 2026
73 of 79 checks passed
@FriederikeHanssen FriederikeHanssen mentioned this pull request Jan 18, 2026
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