UNDER ACTIVE DEVELOPMENT

CGAP Pipeline for statistical analysis of case/control cohort data

This repository contains components for the CGAP pipeline for statistical analysis of case/control cohort data:

• CWL workflow descriptions
• CGAP Portal Workflow and MetaWorkflow objects
• CGAP Portal Software, FileFormat, and FileReference objects
• ECR (Docker) source files, which allow for creation of public Docker images (using docker build) or private dynamically-generated ECR images (using cgap pipeline utils pipeline_deploy)

The pipeline starts from jointly calles, VEP annotated vcf files and produces various result file in text and vcf format. See documentation for details.

cgap-pipeline-cohort

To build the docker image run

docker build -t cgap/cgap-regenie:0.1.0