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feat: Add SNV variant scoring#103

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feat: Add SNV variant scoring#103
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feat-add-snv-variant-score

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@beatrizsavinhas beatrizsavinhas commented May 13, 2026

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@beatrizsavinhas
feat: Add genmod_score_config param (#99)
20608f2 
### Added

- Add `genmod_score_config` param to be used by
'vcf_annotate_score_genmod' subworkflow in
#97.
@beatrizsavinhas beatrizsavinhas changed the title feat: Add SNV variant score feat: Add SNV variant scoring May 13, 2026
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github-actions Bot commented May 13, 2026

PR checklist

  • Fill in description of the PR and link to any relevant issues.
  • If you've fixed a bug, added a subworkflow or any other code that should be tested, add tests!
  • If you've added a new tool, update citations according to the instructions under Adding Citations.
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • README.md is updated (including authors/contributors).

See Contributing Guidelines for more details on how to contribute according to pipeline conventions.

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github-actions Bot commented May 13, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 20608f2

+| ✅ 173 tests passed       |+
#| ❔  19 tests were ignored |#
!| ❗  12 tests had warnings |!
Details

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in README.md: Include a figure that guides the user through the major workflow steps. Many nf-core
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
  • pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
  • pipeline_todos - TODO string in nextflow.config: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in base.config: Customise requirements for specific processes.

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.2
  • Run at 2026-05-13 14:40:08

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