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javibio-git authored Oct 10, 2024
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# How to Run Your Tool in AnVIL with WDL
# 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 {- .unlisted}

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. If time allows, we’ll emerge with some resources for others to run their non-WDL tool in AnVIL.

## Schedule {- .unlisted}

### Tuesday Nov 12, 2024 (2.5 hours) {-}

| Task | Time & Lead |
|:-------------------------:|:-----------:|
| **Pipelining in AnVIL + WDLs presentation** | **2:15pm - 3:15pm:** Scientific Lead |
| **Brainstorming AnVIL resources for wrapping other tools in WDL** | **3:15pm - 4:00pm:** Scientific Lead & Outreach Coordinator |
| **Hackathon-like effort to develop ideas from brainstorming** | **4:00pm - 4:45pm:** Scientific Lead & Outreach Coordinator |

### Wednesday Nov 13, 2024 (3 hours) {-}

| Task | Time & Lead |
|:-------------------------:|:-----------:|
| **Hackathon-like effort to develop ideas from brainstorming** | **1:00pm - 2:30pm:** Scientific Lead & Outreach Coordinator |
| **Coffee break** | **2:30pm - 3:00pm**|
| **Report Out** | **3:00pm - 4:00pm:** Scientific Lead & Outreach Coordinator |
| **CoFest! recap** | **4:00pm** |

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