CGAP Base Pipelines and Shared Components

This repository contains shared components for CGAP pipelines and general processing pipelines:

• 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)

Pipelines

General Processing:

• MD5 Hash

Quality Control:

• FastQC

Format Manipulation:

• cram to fastq
• bam to fastq

Utilities:

• LiftoverVcf (GATK)
• merge (BCFtools)

For more details check the documentation.

Other Components

The respository also stores CGAP Portal objects that are shared by multiple pipelines.