Dockerized Genomic Processing Pipelines

Genomic data processing pipelines written in Workflow Definition Language (WDL), making use of Docker containers to ensure reproducability and limit time spent setting up a compute environment. The Docker containers used have been curated for usage in the Faryabi Lab processing pipelines, and can be found on Dockerhub.

Setup

Clone this repository to your local machine:

git clone https://github.com/faryabiLab/dockerize-workflows

Dependencies

• Cromwell WDL engine jarfile
• JDK 8+
• Docker

Usage documentation available here.

Tips for troubleshooting common errors can be found here.

Development guide can be found here.