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.