CGAP Upstream Pipeline (and Joint Calling) - Sentieon

This repository contains components for the CGAP upstream pipeline and the joint calling pipeline using Sentieon:

• 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 portal pipeline utils pipeline_deploy)

The upstream pipeline can process paired-end fastq files up to analysis-ready bam files. The joint calling pipeline can jointly call multiple g.vcf files and produces a vcf file as output. Documentation for all CGAP Pipelines can now be found here: https://cgap-pipeline-main.readthedocs.io/en/latest/