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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 are two days of training, a two day meeting, and two to four days of intense collaboration.  The meeting will feature joint & parallel sessions, shared keynotes, poster & demo sessions, birds-of-a-feather, and social events.  GCCBOSC brings together the widest possible community of bioinformatics developers and practitioners into a single event.  GCCBOSC is organized by Oregon Health & Science University and will be at Reed College.

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Tuesday, June 26 • 3:30pm - 6:00pm
GATK4: What's new and how to run it

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Key:  BB | XB |  -  |  -  | GG | 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.
Prerequisites:
  • Mac or Linux computer
  • Java 8 installed and runnable from the command line
  • A workshop bundle downloaded from TBD

Speakers
avatar for Geraldine Van der Auwera

Geraldine Van der Auwera

Associate Director of Outreach and Communications, Broad Institute
I run outreach and communication efforts to the global scientific research community on behalf of the Data Sciences Platform (DSP) at the Broad Institute. My team's efforts include technical support, documentation, social media presence and user education events for users of soft... Read More →


Tuesday June 26, 2018 3:30pm - 6:00pm
Training Venue 2