Add DeepVariant #199
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Add DeepVariant #199
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Pull Request Overview
This PR adds DeepVariant as an alternative variant calling algorithm to the existing HaplotypeCaller pipeline. The implementation allows users to specify which algorithms to run via the algorithm parameter, supporting both HaplotypeCaller and DeepVariant workflows.
Key changes include:
- Creation of modular workflow files for both algorithms
- Addition of DeepVariant-specific modules for variant calling and interval conversion
- Updated configuration and testing infrastructure to support algorithm selection
- Documentation updates reflecting the new dual-algorithm capability
Reviewed Changes
Copilot reviewed 17 out of 18 changed files in this pull request and generated 1 comment.
Show a summary per file
| File | Description |
|---|---|
| main.nf | Refactored to support algorithm selection and separate workflow execution |
| module/workflow-deepvariant.nf | New workflow implementing DeepVariant variant calling pipeline |
| module/workflow-haplotypecaller.nf | Extracted HaplotypeCaller logic into separate workflow module |
| module/deepvariant.nf | New process for running DeepVariant variant calling |
| module/convert-intervals.nf | New process for converting IntervalList format to BED format |
| config/schema.yaml | Added algorithm parameter validation and choices |
| test files | Added test configurations and updated nftest for DeepVariant |
| README.md | Updated documentation to reflect DeepVariant addition |
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Description
Adding DeepVariant as an option for variant calling.
Testing Results
NFTest:
<devdir>/log-nftest-20250807T204112Z.log<devdir>/log-nftest-20250807T204113Z.logChecklist
I have read the code review guidelines and the code review best practice on GitHub check-list.
I have reviewed the Nextflow pipeline standards.
The name of the branch is meaningful and well formatted following the standards, using [AD_username (or 5 letters of AD if AD is too long)]-[brief_description_of_branch].
I have set up or verified the branch protection rule following the github standards before opening this pull request.
I have added my name to the contributors listings in the
manifestblock in thenextflow.configas part of this pull request, am listedalready, or do not wish to be listed. (This acknowledgement is optional.)
I have added the changes included in this pull request to the
CHANGELOG.mdunder the next release version or unreleased, and updated the date.I have updated the version number in the
metadata.yamlandmanifestblock of thenextflow.configfile following semver, or the version number has already been updated. (Leave it unchecked if you are unsure about new version number and discuss it with the infrastructure team in this PR.)I have tested the pipeline on at least one A-mini sample.