CGAP Upstream Pipeline - GATK

This repository contains components for the CGAP upstream pipeline using GATK (Genome Analysis Toolkit):

• 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 pipeline can process paired-end fastq files up to analysis-ready bam files. Documentation for all CGAP Pipelines can now be found here: https://cgap-pipeline-main.readthedocs.io/en/latest/