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Update VEP version to 115.0-0 #2119

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Merged
FriederikeHanssen merged 4 commits into from
Feb 2, 2026
Merged

Update VEP version to 115.0-0 #2119

FriederikeHanssen merged 4 commits into from
Feb 2, 2026

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@FriederikeHanssen
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@FriederikeHanssen FriederikeHanssen commented Feb 1, 2026 •
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Summary

  • Update VEP version parameter from 111.0-0 to 115.0-0 in nextflow.config
  • Update VEP cache version from 114 to 115 in igenomes.config for GRCh38
  • Update ensemblvep module to include perl-math-cdf dependency required for Condel plugin
  • Remove unused vcf_annotate_ensemblvep nf-core subworkflow (replaced by local implementation)

Test plan

  • Verify VEP annotation runs correctly with the new version
  • Test with both local VEP cache and downloaded cache
  • Verify Condel plugin works with the updated container

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github-actions bot commented Feb 1, 2026 •
edited by nf-core-bot
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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.

@FriederikeHanssen
Update VEP version to 115.0-0
c35e6de 
- Update VEP version parameter from 111.0-0 to 115.0-0 in nextflow.config
- Update VEP cache version from 114 to 115 in igenomes.config
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github-actions bot commented Feb 1, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 88f9d01

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

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 3.8.0
  • 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 2026-02-02 11:10:36

@FriederikeHanssen FriederikeHanssen changed the base branch from master to dev February 2, 2026 10:28
@FriederikeHanssen FriederikeHanssen merged commit 37d4e65 into dev Feb 2, 2026
40 of 42 checks passed
@FriederikeHanssen FriederikeHanssen deleted the vep-version branch February 2, 2026 11:24
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@maxulysse maxulysse maxulysse approved these changes

@jfy133 jfy133 jfy133 approved these changes

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3 participants

@FriederikeHanssen @maxulysse @jfy133