wrap-tool.Rmd

# 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

## 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.  

## 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](https://anvil.terra.bio/#workspaces/acc2024-cofest-wdl/AnVIL_CoFest2024_Wrap-a-tool-in-WDL).

## Prep work

Participants on this topics should:

1. Download the Dockstore desktop app from [https://www.docker.com/products/docker-desktop/](https://www.docker.com/products/docker-desktop/).
2. Register for a DockerHub account at [https://hub.docker.com/](https://hub.docker.com/).

## Schedule

### 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 |

### 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 |

## Slides

Slides for this topic can be found [here](https://docs.google.com/presentation/d/1s83zP55EZTl0HmXCp0mO97JQmDNR1sTiDr_931aO6RE/edit?usp=sharing).