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 utilspipeline_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/