# CWL wrappers for UW GENESIS tools

This repository contains CWL workflows for the following UW-GAC GENESIS pipelines for TopMED data:

1. VCF to GDS converter [![VCF 2 GDS test][vcf2gdstest-badge]][vcf2gdstest]
1. Null Model (Association testing) [![NullModel][nullmodeltest-badge]][nullmodeltest]
1. Single Variant (Association testing) [![SVA test][svatest-badge]][svatest]

[vcf2gdstest-badge]: https://github.com/kaushik-work/uw-genesis-topmed-cwl/workflows/vcf2gds/badge.svg
[vcf2gdstest]: https://github.com/kaushik-work/uw-genesis-topmed-cwl/actions?query=workflow%3Avcf2gds

[nullmodeltest-badge]: https://github.com/kaushik-work/uw-genesis-topmed-cwl/workflows/nullmodel/badge.svg
[nullmodeltest]: https://github.com/kaushik-work/uw-genesis-topmed-cwl/actions?query=workflow%3Anullmodel

[svatest-badge]: https://github.com/kaushik-work/uw-genesis-topmed-cwl/workflows/sva/badge.svg
[svatest]: https://github.com/kaushik-work/uw-genesis-topmed-cwl/actions?query=workflow%3Asva

The CWL wraps the tools described in https://github.com/UW-GAC/analysis_pipeline