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## collate en_US.UTF-8
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## tz Etc/UTC
## date 2024-10-08
## date 2024-10-10
## pandoc 3.1.1 @ /usr/local/bin/ (via rmarkdown)
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## ─ Packages ───────────────────────────────────────────────────────────────────
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## collate en_US.UTF-8
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## date 2024-10-08
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## pandoc 3.1.1 @ /usr/local/bin/ (via rmarkdown)
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<meta name="date" content="2024-10-08" />
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<h1><span class="header-section-number">Chapter 3</span> How to Run Your Tool in AnVIL with WDL<a href="how-to-run-your-tool-in-anvil-with-wdl.html#how-to-run-your-tool-in-anvil-with-wdl" class="anchor-section" aria-label="Anchor link to header"></a></h1>
<p>Led by: Allie Cliffe, Broad Institute of MIT and Harvard</p>
<p>AnVIL Outreach coordinator: Javier Carpinteyro-Ponce</p>
<p>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.</p>

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</div>
<div id="header">
<h1 class="title">AnVIL CoFests! 2024</h1>
<p class="date"><em>October 08, 2024</em></p>
<p class="date"><em>October 10, 2024</em></p>
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<div id="what-are-cofests" class="section level1 unnumbered hasAnchor">
<h1>What are CoFests!?<a href="index.html#what-are-cofests" class="anchor-section" aria-label="Anchor link to header"></a></h1>
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---
title: "AnVIL CoFests! 2024"
date: "October 08, 2024"
date: "October 10, 2024"
site: bookdown::bookdown_site
documentclass: book
bibliography: book.bib
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Led by: Allie Cliffe, Broad Institute of MIT and Harvard

AnVIL Outreach coordinator: Javier Carpinteyro-Ponce


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.

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