→ Schedule, Slides, Tutorial, VideoThis is the first session of a two part training. Please register for both. The second session is on Sunday.
In this session, we'll use Janis (a Python workflow framework) to build a GATK pipeline to call variants. We'll show how Janis workflows can be translated to CWL and WDL, and how to use the Janis assistant to run these pipelines in CWLTool and Cromwell.
Through the use of containers, the pipeline produced in this workshop can be run locally, on HPCs with Singularity or through cloud vendors (such as Google Cloud and AWS).
Prerequisites- Some basic Python is preferred
- Installed Software: Docker, Python 3.6+
