Chapter 3 How to Run Your Tool in AnVIL with WDL

Led by: Allie Cliffe, Broad Institute of MIT and Harvard

AnVIL Outreach coordinator: Javier Carpinteyro-Ponce

3.1 About

Workflow Description Language (WDL) not in your programming skillset? No problem! Learn to wrap your pipelining tool in WDL and run it in an AnVIL workspace in this CoFest! session. We’ll go over WDL basics and how to run pipelines in AnVIL, then walk through how to run your own Unix/Python/R script. Along the way, you’ll write a WDL and build a custom Docker to run it with. Come and wrap a tool of interest! All experience levels are welcome. We’ll brainstorm and, if time allows, we’ll create resources (tutorials? AnVIL book? Cheat sheet?) for others to use to run their non-WDL tool in AnVIL.

3.2 Workspace

The workspace for this topic can be found at https://anvil.terra.bio/#workspaces/acc2024-cofest-wdl/AnVIL_CoFest2024_Wrap-a-tool-in-WDL.

3.3 Prep work

Participants on this topics should:

Download the Dockstore desktop app from https://www.docker.com/products/docker-desktop/.
Register for a DockerHub account at https://hub.docker.com/.

3.4 Schedule

3.4.1 Tuesday Nov 12, 2024 (2.5 hours)

Task	Time
Pipelining in AnVIL + WDLs presentation	2:15pm - 3:00pm
Running a WDL and running Python script wrapped in WDL	3:00pm - 4:00pm
Brainstorming AnVIL resources for wrapping other tools in WDL	4:00pm - 4:45pm

3.4.2 Wednesday Nov 13, 2024 (3 hours)

Task	Time
Hackathon-like effort to develop ideas from brainstorming	1:00pm - 2:30pm
Coffee break	2:30pm - 3:00pm
Report Out	3:00pm - 4:00pm
CoFest! recap	4:00pm

3.5 Slides

Slides for this topic can be found here.