Loading…
BCC2020 has ended
➞ Set your timezone before doing anything else on this site (home page, on the right)
Limit what is shown by Type, Category, or Hemisphere
Registration closed July 15.

BCC2020 is online, global, and affordable. The meeting and training are now done, and the CoFest is under way.

The 2020 Bioinformatics Community Conference brings together the Bioinformatics Open Source Conference (BOSC) and the Galaxy Community Conference into a single event featuring training, a meeting, and a CollaborationFest. Events run from July 17 through July 25, and is held in both the eastern and western hemispheres.

Back To Schedule
Saturday, July 18 • 00:16 - 02:45
Produce a portable germline variant-calling pipeline in CWL and WDL using Janis and GATK I

Sign up or log in to save this to your schedule, view media, leave feedback and see who's attending!

 ScheduleSlides, TutorialVideo

This 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+

Speakers
avatar for Michael Franklin

Michael Franklin

Research Software Engineer, University of Melbourne
I'm a research software engineer at the University of Melbourne / Peter MacCallum Cancer Centre who's interested in all things pipelines! I develop Janis, a workflow assistant that generates CWL and WDL. I'm also interested in general programming, specifically web (React) and database-y... Read More →
RL

Richard Lupat

Peter MacCallum Cancer Centre


Saturday July 18, 2020 00:16 - 02:45 EDT
Training E