GCC BOSC 2018 has ended
The 2018 Galaxy Community Conference (GCC2018) and Bioinformatics Open Source Conference 2018 (BOSC2018) are meeting together in Portland, Oregon, United States, June 25-30, 2018.  There will be two days of training, a two+ day meeting, and four days of intense collaboration.  The meeting features joint & parallel sessions, shared keynotes, poster & demo sessions, birds-of-a-feather, and social events.  GCCBOSC is organized by Oregon Health & Science University and will be at Reed College.

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Tuesday, June 26 • 9:00am - 11:30am
WDL: the Workflow Description Language

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Training Materials

Key:  -  | XB | IP | TD |  -  | CL

The advent of open, portable workflow languages is an exciting development which allows for the definition of a workflow to be decoupled from the execution. One can create workflows which can run unmodified on local compute, HPC clusters, or the cloud. As these languages are not tied to a specific execution environment, the descriptions can easily be shared, discovered and even composed together to form more complex workflows. The Workflow Description Language (WDL) is an open, community driven standard that is designed from the ground up as a human-readable and -writable way to express portable tasks and workflows.
In this session we’ll walk through the lifecycle of writing, sharing and discovering portable workflows in WDL. We’ll introduce the WDL syntax. You’ll learn how to write and run a workflow locally. We’ll demonstrate how to use EPAM’s Pipeline Builder toolto visualize WDL workflows. We’ll look at Dockstore, an open platform where one can publish, share and discover workflows. Finally we’ll put everything together and see how we can compose workflows we find on Dockstore together with our own additions to create new, more powerful workflows.
  • Mac or Linux computer
  • Java 8 installed and runnable from the command line
  • A workshop bundle downloaded from TBD

avatar for Geraldine Van der Auwera

Geraldine Van der Auwera

Director of Outreach and Communications, Broad Institute Data Sciences Platform
I direct outreach and communication efforts for the software and services developed by the Data Sciences Platform at the Broad Institute, which include GATK, the Broad's open source toolkit for variant discovery analysis; the Cromwell/WDL workflow management system; and Terra.bio... Read More →
avatar for Jeff Gentry

Jeff Gentry

Senior Principal Software Engineer, Broad Institute
Jeff leads the development of the Cromwell workflow engine at the Broad Institute and is in the leadership groups for both the Workflow Description Language (WDL) as well as the Common Workflow Language (CWL). He has over 15 years of experience developing software for the bioinformatics... Read More →

Chris Llanwarne

Broad Institute

Tuesday June 26, 2018 9:00am - 11:30am PDT
Vollum Lounge Vollum College Center, Reed Campus