CGAP Pipeline for Germline Single Nucleotide Variants and small INDELs

This repository contains components for the CGAP pipeline for Single Nucleotide Variants (SNVs) and small insertions/delitions (INDELs) in germline 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 portal pipeline utils pipeline_deploy)

The pipeline starts from analysis-ready bam files and produces g.vcf and vcf files containing calls for SNVs and small INDELs as output. Documentation for all CGAP Pipelines can now be found here: https://cgap-pipeline-main.readthedocs.io/en/latest/