From 1f2e2c608a75e529fd3854a787dc8bca80fca14c Mon Sep 17 00:00:00 2001
From: "github-actions[bot]" <github-actions[bot]@users.noreply.github.com>
Date: Tue, 24 Sep 2024 16:37:07 +0000
Subject: [PATCH] Render bookdown

---
 docs/404.html                                 |   4 +-
 docs/About.md                                 |   2 +-
 docs/about-the-authors.html                   |  10 +-
 ...ow-to-run-your-tool-in-anvil-with-wdl.html | 209 ++++++++++++++++++
 docs/index.html                               |   6 +-
 docs/index.md                                 |   2 +-
 docs/organizer-guide.html                     |   4 +-
 docs/polygenic-risk-score-analysis.html       |   8 +-
 docs/reference-keys.txt                       |   2 +-
 docs/references.html                          |   4 +-
 docs/scalable-ml-and-data-science.html        |   4 +-
 docs/search_index.json                        |   2 +-
 docs/wrap-tool.md                             |   2 +-
 13 files changed, 234 insertions(+), 25 deletions(-)
 create mode 100644 docs/how-to-run-your-tool-in-anvil-with-wdl.html

diff --git a/docs/404.html b/docs/404.html
index 439fbab..e386740 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -22,7 +22,7 @@
 
 
 
-<meta name="date" content="2024-09-18" />
+<meta name="date" content="2024-09-24" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -94,7 +94,7 @@
 <li class="part"><span><b>Topics</b></span></li>
 <li class="chapter" data-level="1" data-path="scalable-ml-and-data-science.html"><a href="scalable-ml-and-data-science.html"><i class="fa fa-check"></i><b>1</b> Scalable ML and Data Science</a></li>
 <li class="chapter" data-level="2" data-path="polygenic-risk-score-analysis.html"><a href="polygenic-risk-score-analysis.html"><i class="fa fa-check"></i><b>2</b> Polygenic Risk Score Analysis</a></li>
-<li class="chapter" data-level="3" data-path="wrap-a-tool-with-wdl.html"><a href="wrap-a-tool-with-wdl.html"><i class="fa fa-check"></i><b>3</b> Wrap a Tool with WDL</a></li>
+<li class="chapter" data-level="3" data-path="how-to-run-your-tool-in-anvil-with-wdl.html"><a href="how-to-run-your-tool-in-anvil-with-wdl.html"><i class="fa fa-check"></i><b>3</b> How to Run Your Tool in AnVIL with WDL</a></li>
 <li class="chapter" data-level="" data-path="about-the-authors.html"><a href="about-the-authors.html"><i class="fa fa-check"></i>About the Authors</a></li>
 <li class="chapter" data-level="4" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>4</b> References</a></li>
 <li class="divider"></li>
diff --git a/docs/About.md b/docs/About.md
index e270251..c5784e7 100644
--- a/docs/About.md
+++ b/docs/About.md
@@ -53,7 +53,7 @@ These credits are based on our [course contributors table guidelines](https://gi
 ##  collate  en_US.UTF-8
 ##  ctype    en_US.UTF-8
 ##  tz       Etc/UTC
-##  date     2024-09-18
+##  date     2024-09-24
 ##  pandoc   3.1.1 @ /usr/local/bin/ (via rmarkdown)
 ## 
 ## ─ Packages ───────────────────────────────────────────────────────────────────
diff --git a/docs/about-the-authors.html b/docs/about-the-authors.html
index 38ed90b..3599f8f 100644
--- a/docs/about-the-authors.html
+++ b/docs/about-the-authors.html
@@ -22,14 +22,14 @@
 
 
 
-<meta name="date" content="2024-09-18" />
+<meta name="date" content="2024-09-24" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
   <meta name="apple-mobile-web-app-status-bar-style" content="black" />
   
   <link rel="shortcut icon" href="assets/AnVIL_style/anvil_favicon.ico" type="image/x-icon" />
-<link rel="prev" href="wrap-a-tool-with-wdl.html"/>
+<link rel="prev" href="how-to-run-your-tool-in-anvil-with-wdl.html"/>
 <link rel="next" href="references.html"/>
 <script src="libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
 <script src="https://cdn.jsdelivr.net/npm/fuse.js@6.4.6/dist/fuse.min.js"></script>
@@ -94,7 +94,7 @@
 <li class="part"><span><b>Topics</b></span></li>
 <li class="chapter" data-level="1" data-path="scalable-ml-and-data-science.html"><a href="scalable-ml-and-data-science.html"><i class="fa fa-check"></i><b>1</b> Scalable ML and Data Science</a></li>
 <li class="chapter" data-level="2" data-path="polygenic-risk-score-analysis.html"><a href="polygenic-risk-score-analysis.html"><i class="fa fa-check"></i><b>2</b> Polygenic Risk Score Analysis</a></li>
-<li class="chapter" data-level="3" data-path="wrap-a-tool-with-wdl.html"><a href="wrap-a-tool-with-wdl.html"><i class="fa fa-check"></i><b>3</b> Wrap a Tool with WDL</a></li>
+<li class="chapter" data-level="3" data-path="how-to-run-your-tool-in-anvil-with-wdl.html"><a href="how-to-run-your-tool-in-anvil-with-wdl.html"><i class="fa fa-check"></i><b>3</b> How to Run Your Tool in AnVIL with WDL</a></li>
 <li class="chapter" data-level="" data-path="about-the-authors.html"><a href="about-the-authors.html"><i class="fa fa-check"></i>About the Authors</a></li>
 <li class="chapter" data-level="4" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>4</b> References</a></li>
 <li class="divider"></li>
@@ -275,7 +275,7 @@ <h1>About the Authors<a href="about-the-authors.html#about-the-authors" class="a
 ##  collate  en_US.UTF-8
 ##  ctype    en_US.UTF-8
 ##  tz       Etc/UTC
-##  date     2024-09-18
+##  date     2024-09-24
 ##  pandoc   3.1.1 @ /usr/local/bin/ (via rmarkdown)
 ## 
 ## ─ Packages ───────────────────────────────────────────────────────────────────
@@ -354,7 +354,7 @@ <h1>About the Authors<a href="about-the-authors.html#about-the-authors" class="a
           </div>
         </div>
       </div>
-<a href="wrap-a-tool-with-wdl.html" class="navigation navigation-prev " aria-label="Previous page"><i class="fa fa-angle-left"></i></a>
+<a href="how-to-run-your-tool-in-anvil-with-wdl.html" class="navigation navigation-prev " aria-label="Previous page"><i class="fa fa-angle-left"></i></a>
 <a href="references.html" class="navigation navigation-next " aria-label="Next page"><i class="fa fa-angle-right"></i></a>
     </div>
   </div>
diff --git a/docs/how-to-run-your-tool-in-anvil-with-wdl.html b/docs/how-to-run-your-tool-in-anvil-with-wdl.html
new file mode 100644
index 0000000..a463847
--- /dev/null
+++ b/docs/how-to-run-your-tool-in-anvil-with-wdl.html
@@ -0,0 +1,209 @@
+<!DOCTYPE html>
+<html lang="" xml:lang="">
+<head>
+
+  <meta charset="utf-8" />
+  <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+  <title>Chapter 3 How to Run Your Tool in AnVIL with WDL | AnVIL CoFests! 2024</title>
+  <meta name="description" content="Description about Course/Book." />
+  <meta name="generator" content="bookdown 0.39.1 and GitBook 2.6.7" />
+
+  <meta property="og:title" content="Chapter 3 How to Run Your Tool in AnVIL with WDL | AnVIL CoFests! 2024" />
+  <meta property="og:type" content="book" />
+  
+  <meta property="og:description" content="Description about Course/Book." />
+  
+
+  <meta name="twitter:card" content="summary" />
+  <meta name="twitter:title" content="Chapter 3 How to Run Your Tool in AnVIL with WDL | AnVIL CoFests! 2024" />
+  
+  <meta name="twitter:description" content="Description about Course/Book." />
+  
+
+
+
+<meta name="date" content="2024-09-24" />
+
+  <meta name="viewport" content="width=device-width, initial-scale=1" />
+  <meta name="apple-mobile-web-app-capable" content="yes" />
+  <meta name="apple-mobile-web-app-status-bar-style" content="black" />
+  
+  <link rel="shortcut icon" href="assets/AnVIL_style/anvil_favicon.ico" type="image/x-icon" />
+<link rel="prev" href="polygenic-risk-score-analysis.html"/>
+<link rel="next" href="about-the-authors.html"/>
+<script src="libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
+<script src="https://cdn.jsdelivr.net/npm/fuse.js@6.4.6/dist/fuse.min.js"></script>
+<link href="libs/gitbook-2.6.7/css/style.css" rel="stylesheet" />
+<link href="libs/gitbook-2.6.7/css/plugin-table.css" rel="stylesheet" />
+<link href="libs/gitbook-2.6.7/css/plugin-bookdown.css" rel="stylesheet" />
+<link href="libs/gitbook-2.6.7/css/plugin-highlight.css" rel="stylesheet" />
+<link href="libs/gitbook-2.6.7/css/plugin-search.css" rel="stylesheet" />
+<link href="libs/gitbook-2.6.7/css/plugin-fontsettings.css" rel="stylesheet" />
+<link href="libs/gitbook-2.6.7/css/plugin-clipboard.css" rel="stylesheet" />
+
+
+
+
+
+
+
+
+<link href="libs/anchor-sections-1.1.0/anchor-sections.css" rel="stylesheet" />
+<link href="libs/anchor-sections-1.1.0/anchor-sections-hash.css" rel="stylesheet" />
+<script src="libs/anchor-sections-1.1.0/anchor-sections.js"></script>
+  
+<!-- Google tag (gtag.js) -->
+<script async src="https://www.googletagmanager.com/gtag/js?id=G-ZTKJE9VK99"></script>
+<script>
+  window.dataLayer = window.dataLayer || [];
+  function gtag(){dataLayer.push(arguments);}
+  gtag('js', new Date());
+
+  gtag('config', 'G-ZTKJE9VK99');
+</script>
+
+
+
+<style type="text/css">
+  
+  div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
+</style>
+
+<link rel="stylesheet" href="assets/style.css" type="text/css" />
+<link rel="stylesheet" href="assets/AnVIL_style/anvil.css" type="text/css" />
+</head>
+
+<body>
+
+
+
+  <div class="book without-animation with-summary font-size-2 font-family-1" data-basepath=".">
+
+    <div class="book-summary">
+      <nav role="navigation">
+
+<ul class="summary">
+<a href="https://anvilproject.org/" target="_blank"><img src="assets/AnVIL_style/logo-anvil.png" style="width: 80%; padding-left: 15px; padding-top: 8px;"</a>
+
+<li class="divider"></li>
+<li class="chapter" data-level="" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i>What are CoFests!?</a></li>
+<li class="chapter" data-level="" data-path="organizer-guide.html"><a href="organizer-guide.html"><i class="fa fa-check"></i>Organizer Guide</a>
+<ul>
+<li class="chapter" data-level="" data-path="organizer-guide.html"><a href="organizer-guide.html#final-product-report-out"><i class="fa fa-check"></i>Final Product / Report Out</a></li>
+</ul></li>
+<li class="part"><span><b>Topics</b></span></li>
+<li class="chapter" data-level="1" data-path="scalable-ml-and-data-science.html"><a href="scalable-ml-and-data-science.html"><i class="fa fa-check"></i><b>1</b> Scalable ML and Data Science</a></li>
+<li class="chapter" data-level="2" data-path="polygenic-risk-score-analysis.html"><a href="polygenic-risk-score-analysis.html"><i class="fa fa-check"></i><b>2</b> Polygenic Risk Score Analysis</a></li>
+<li class="chapter" data-level="3" data-path="how-to-run-your-tool-in-anvil-with-wdl.html"><a href="how-to-run-your-tool-in-anvil-with-wdl.html"><i class="fa fa-check"></i><b>3</b> How to Run Your Tool in AnVIL with WDL</a></li>
+<li class="chapter" data-level="" data-path="about-the-authors.html"><a href="about-the-authors.html"><i class="fa fa-check"></i>About the Authors</a></li>
+<li class="chapter" data-level="4" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>4</b> References</a></li>
+<li class="divider"></li>
+<p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown by: </a> </p>
+<p style="text-align:center;"> <a href="https://hutchdatascience.org/"> The Fred Hutch Data Science Lab </a></p>
+<a href="https://hutchdatascience.org/" target="_blank"><img src="https://raw.githubusercontent.com/jhudsl/OTTR_Template/main/style-sets/fhdasl/copy_to_assets/big-dasl-stacked.png" style="width: 80%; padding-left: 34px; padding-top: 8px;"</a>
+<p style="text-align:center; font-size: 12px;"> <a href="https://github.com/rstudio4edu/rstudio4edu-book/"> Style adapted from: rstudio4edu-book </a> <a href ="https://creativecommons.org/licenses/by/2.0/"> (CC-BY 2.0) </a></p>
+<p style="padding-left: 40px;"><div class="trapezoid" style = "padding-left: 40px;"><span><a href="https://docs.google.com/forms/d/e/1FAIpQLScrDVb_utm55pmb_SHx-RgELTEbCCWdLea0T3IzS0Oj00GE4w/viewform?usp=pp_url&entry.1565230805=AnVIL+CoFests!+2024"> Click here to provide feedback</a> <img src="assets/itcr_arrow.png" style=" width: 10%" ></span></div></p>
+
+</ul>
+
+      </nav>
+    </div>
+
+    <div class="book-body">
+      <div class="body-inner">
+        <div class="book-header" role="navigation">
+          <h1>
+            <i class="fa fa-circle-o-notch fa-spin"></i><a href="./">AnVIL CoFests! 2024</a>
+          </h1>
+        </div>
+
+        <div class="page-wrapper" tabindex="-1" role="main">
+          <div class="page-inner">
+
+            <section class="normal" id="section-">
+<head>
+  <meta name="viewport" content="width=device-width,minimum-scale=1.0,maximum-scale=10.0,initial-scale=1.0">
+  <!--script src="https://kit.fontawesome.com/6a26f47516.js"></script-->
+  <!--<script src="assets/hideOutput.js"></script>-->
+</head>
+        
+
+
+<div class="hero-image-container"> 
+  <img class= "hero-image" src="assets/AnVIL_style/dasl_thin_main_image.png">
+</div>
+<div id="how-to-run-your-tool-in-anvil-with-wdl" class="section level1 hasAnchor" number="3">
+<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>
+
+</div>
+<hr>
+<center> 
+  <div class="footer">
+      All illustrations <a href="https://creativecommons.org/licenses/by/4.0/">CC-BY. </a>
+      <br>
+      All other materials <a href= "https://creativecommons.org/licenses/by/4.0/"> CC-BY </a> unless noted otherwise.
+  </div>
+</center>
+            </section>
+
+          </div>
+        </div>
+      </div>
+<a href="polygenic-risk-score-analysis.html" class="navigation navigation-prev " aria-label="Previous page"><i class="fa fa-angle-left"></i></a>
+<a href="about-the-authors.html" class="navigation navigation-next " aria-label="Next page"><i class="fa fa-angle-right"></i></a>
+    </div>
+  </div>
+<script src="libs/gitbook-2.6.7/js/app.min.js"></script>
+<script src="libs/gitbook-2.6.7/js/clipboard.min.js"></script>
+<script src="libs/gitbook-2.6.7/js/plugin-search.js"></script>
+<script src="libs/gitbook-2.6.7/js/plugin-sharing.js"></script>
+<script src="libs/gitbook-2.6.7/js/plugin-fontsettings.js"></script>
+<script src="libs/gitbook-2.6.7/js/plugin-bookdown.js"></script>
+<script src="libs/gitbook-2.6.7/js/jquery.highlight.js"></script>
+<script src="libs/gitbook-2.6.7/js/plugin-clipboard.js"></script>
+<script>
+gitbook.require(["gitbook"], function(gitbook) {
+gitbook.start({
+"sharing": {
+"github": false,
+"facebook": true,
+"twitter": true,
+"linkedin": false,
+"weibo": false,
+"instapaper": false,
+"vk": false,
+"whatsapp": false,
+"all": ["facebook", "twitter", "linkedin", "weibo", "instapaper"]
+},
+"fontsettings": {
+"theme": "white",
+"family": "sans",
+"size": 2
+},
+"edit": {
+"link": null,
+"text": null
+},
+"history": {
+"link": null,
+"text": null
+},
+"view": {
+"link": null,
+"text": null
+},
+"download": null,
+"search": {
+"engine": "fuse",
+"options": null
+},
+"toc": {
+"collapse": "section"
+}
+});
+});
+</script>
+
+</body>
+
+</html>
diff --git a/docs/index.html b/docs/index.html
index 38cbe85..8cc2a41 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -22,7 +22,7 @@
 
 
 
-<meta name="date" content="2024-09-18" />
+<meta name="date" content="2024-09-24" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -94,7 +94,7 @@
 <li class="part"><span><b>Topics</b></span></li>
 <li class="chapter" data-level="1" data-path="scalable-ml-and-data-science.html"><a href="scalable-ml-and-data-science.html"><i class="fa fa-check"></i><b>1</b> Scalable ML and Data Science</a></li>
 <li class="chapter" data-level="2" data-path="polygenic-risk-score-analysis.html"><a href="polygenic-risk-score-analysis.html"><i class="fa fa-check"></i><b>2</b> Polygenic Risk Score Analysis</a></li>
-<li class="chapter" data-level="3" data-path="wrap-a-tool-with-wdl.html"><a href="wrap-a-tool-with-wdl.html"><i class="fa fa-check"></i><b>3</b> Wrap a Tool with WDL</a></li>
+<li class="chapter" data-level="3" data-path="how-to-run-your-tool-in-anvil-with-wdl.html"><a href="how-to-run-your-tool-in-anvil-with-wdl.html"><i class="fa fa-check"></i><b>3</b> How to Run Your Tool in AnVIL with WDL</a></li>
 <li class="chapter" data-level="" data-path="about-the-authors.html"><a href="about-the-authors.html"><i class="fa fa-check"></i>About the Authors</a></li>
 <li class="chapter" data-level="4" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>4</b> References</a></li>
 <li class="divider"></li>
@@ -134,7 +134,7 @@ <h1>
 </div>
 <div id="header">
 <h1 class="title">AnVIL CoFests! 2024</h1>
-<p class="date"><em>September 18, 2024</em></p>
+<p class="date"><em>September 24, 2024</em></p>
 </div>
 <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>
diff --git a/docs/index.md b/docs/index.md
index 466b69e..91da717 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -1,6 +1,6 @@
 ---
 title: "AnVIL CoFests! 2024"
-date: "September 18, 2024"
+date: "September 24, 2024"
 site: bookdown::bookdown_site
 documentclass: book
 bibliography: book.bib
diff --git a/docs/organizer-guide.html b/docs/organizer-guide.html
index e274f5d..6523746 100644
--- a/docs/organizer-guide.html
+++ b/docs/organizer-guide.html
@@ -22,7 +22,7 @@
 
 
 
-<meta name="date" content="2024-09-18" />
+<meta name="date" content="2024-09-24" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -94,7 +94,7 @@
 <li class="part"><span><b>Topics</b></span></li>
 <li class="chapter" data-level="1" data-path="scalable-ml-and-data-science.html"><a href="scalable-ml-and-data-science.html"><i class="fa fa-check"></i><b>1</b> Scalable ML and Data Science</a></li>
 <li class="chapter" data-level="2" data-path="polygenic-risk-score-analysis.html"><a href="polygenic-risk-score-analysis.html"><i class="fa fa-check"></i><b>2</b> Polygenic Risk Score Analysis</a></li>
-<li class="chapter" data-level="3" data-path="wrap-a-tool-with-wdl.html"><a href="wrap-a-tool-with-wdl.html"><i class="fa fa-check"></i><b>3</b> Wrap a Tool with WDL</a></li>
+<li class="chapter" data-level="3" data-path="how-to-run-your-tool-in-anvil-with-wdl.html"><a href="how-to-run-your-tool-in-anvil-with-wdl.html"><i class="fa fa-check"></i><b>3</b> How to Run Your Tool in AnVIL with WDL</a></li>
 <li class="chapter" data-level="" data-path="about-the-authors.html"><a href="about-the-authors.html"><i class="fa fa-check"></i>About the Authors</a></li>
 <li class="chapter" data-level="4" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>4</b> References</a></li>
 <li class="divider"></li>
diff --git a/docs/polygenic-risk-score-analysis.html b/docs/polygenic-risk-score-analysis.html
index cd3b03c..7522b82 100644
--- a/docs/polygenic-risk-score-analysis.html
+++ b/docs/polygenic-risk-score-analysis.html
@@ -22,7 +22,7 @@
 
 
 
-<meta name="date" content="2024-09-18" />
+<meta name="date" content="2024-09-24" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -30,7 +30,7 @@
   
   <link rel="shortcut icon" href="assets/AnVIL_style/anvil_favicon.ico" type="image/x-icon" />
 <link rel="prev" href="scalable-ml-and-data-science.html"/>
-<link rel="next" href="wrap-a-tool-with-wdl.html"/>
+<link rel="next" href="how-to-run-your-tool-in-anvil-with-wdl.html"/>
 <script src="libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
 <script src="https://cdn.jsdelivr.net/npm/fuse.js@6.4.6/dist/fuse.min.js"></script>
 <link href="libs/gitbook-2.6.7/css/style.css" rel="stylesheet" />
@@ -94,7 +94,7 @@
 <li class="part"><span><b>Topics</b></span></li>
 <li class="chapter" data-level="1" data-path="scalable-ml-and-data-science.html"><a href="scalable-ml-and-data-science.html"><i class="fa fa-check"></i><b>1</b> Scalable ML and Data Science</a></li>
 <li class="chapter" data-level="2" data-path="polygenic-risk-score-analysis.html"><a href="polygenic-risk-score-analysis.html"><i class="fa fa-check"></i><b>2</b> Polygenic Risk Score Analysis</a></li>
-<li class="chapter" data-level="3" data-path="wrap-a-tool-with-wdl.html"><a href="wrap-a-tool-with-wdl.html"><i class="fa fa-check"></i><b>3</b> Wrap a Tool with WDL</a></li>
+<li class="chapter" data-level="3" data-path="how-to-run-your-tool-in-anvil-with-wdl.html"><a href="how-to-run-your-tool-in-anvil-with-wdl.html"><i class="fa fa-check"></i><b>3</b> How to Run Your Tool in AnVIL with WDL</a></li>
 <li class="chapter" data-level="" data-path="about-the-authors.html"><a href="about-the-authors.html"><i class="fa fa-check"></i>About the Authors</a></li>
 <li class="chapter" data-level="4" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>4</b> References</a></li>
 <li class="divider"></li>
@@ -150,7 +150,7 @@ <h1><span class="header-section-number">Chapter 2</span> Polygenic Risk Score An
         </div>
       </div>
 <a href="scalable-ml-and-data-science.html" class="navigation navigation-prev " aria-label="Previous page"><i class="fa fa-angle-left"></i></a>
-<a href="wrap-a-tool-with-wdl.html" class="navigation navigation-next " aria-label="Next page"><i class="fa fa-angle-right"></i></a>
+<a href="how-to-run-your-tool-in-anvil-with-wdl.html" class="navigation navigation-next " aria-label="Next page"><i class="fa fa-angle-right"></i></a>
     </div>
   </div>
 <script src="libs/gitbook-2.6.7/js/app.min.js"></script>
diff --git a/docs/reference-keys.txt b/docs/reference-keys.txt
index 6d8e1bb..a0eb719 100644
--- a/docs/reference-keys.txt
+++ b/docs/reference-keys.txt
@@ -1,4 +1,4 @@
 scalable-ml-and-data-science
 polygenic-risk-score-analysis
-wrap-a-tool-with-wdl
+how-to-run-your-tool-in-anvil-with-wdl
 references
diff --git a/docs/references.html b/docs/references.html
index c8d5f46..9b10e85 100644
--- a/docs/references.html
+++ b/docs/references.html
@@ -22,7 +22,7 @@
 
 
 
-<meta name="date" content="2024-09-18" />
+<meta name="date" content="2024-09-24" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -94,7 +94,7 @@
 <li class="part"><span><b>Topics</b></span></li>
 <li class="chapter" data-level="1" data-path="scalable-ml-and-data-science.html"><a href="scalable-ml-and-data-science.html"><i class="fa fa-check"></i><b>1</b> Scalable ML and Data Science</a></li>
 <li class="chapter" data-level="2" data-path="polygenic-risk-score-analysis.html"><a href="polygenic-risk-score-analysis.html"><i class="fa fa-check"></i><b>2</b> Polygenic Risk Score Analysis</a></li>
-<li class="chapter" data-level="3" data-path="wrap-a-tool-with-wdl.html"><a href="wrap-a-tool-with-wdl.html"><i class="fa fa-check"></i><b>3</b> Wrap a Tool with WDL</a></li>
+<li class="chapter" data-level="3" data-path="how-to-run-your-tool-in-anvil-with-wdl.html"><a href="how-to-run-your-tool-in-anvil-with-wdl.html"><i class="fa fa-check"></i><b>3</b> How to Run Your Tool in AnVIL with WDL</a></li>
 <li class="chapter" data-level="" data-path="about-the-authors.html"><a href="about-the-authors.html"><i class="fa fa-check"></i>About the Authors</a></li>
 <li class="chapter" data-level="4" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>4</b> References</a></li>
 <li class="divider"></li>
diff --git a/docs/scalable-ml-and-data-science.html b/docs/scalable-ml-and-data-science.html
index 3826415..77741d0 100644
--- a/docs/scalable-ml-and-data-science.html
+++ b/docs/scalable-ml-and-data-science.html
@@ -22,7 +22,7 @@
 
 
 
-<meta name="date" content="2024-09-18" />
+<meta name="date" content="2024-09-24" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1" />
   <meta name="apple-mobile-web-app-capable" content="yes" />
@@ -94,7 +94,7 @@
 <li class="part"><span><b>Topics</b></span></li>
 <li class="chapter" data-level="1" data-path="scalable-ml-and-data-science.html"><a href="scalable-ml-and-data-science.html"><i class="fa fa-check"></i><b>1</b> Scalable ML and Data Science</a></li>
 <li class="chapter" data-level="2" data-path="polygenic-risk-score-analysis.html"><a href="polygenic-risk-score-analysis.html"><i class="fa fa-check"></i><b>2</b> Polygenic Risk Score Analysis</a></li>
-<li class="chapter" data-level="3" data-path="wrap-a-tool-with-wdl.html"><a href="wrap-a-tool-with-wdl.html"><i class="fa fa-check"></i><b>3</b> Wrap a Tool with WDL</a></li>
+<li class="chapter" data-level="3" data-path="how-to-run-your-tool-in-anvil-with-wdl.html"><a href="how-to-run-your-tool-in-anvil-with-wdl.html"><i class="fa fa-check"></i><b>3</b> How to Run Your Tool in AnVIL with WDL</a></li>
 <li class="chapter" data-level="" data-path="about-the-authors.html"><a href="about-the-authors.html"><i class="fa fa-check"></i>About the Authors</a></li>
 <li class="chapter" data-level="4" data-path="references.html"><a href="references.html"><i class="fa fa-check"></i><b>4</b> References</a></li>
 <li class="divider"></li>
diff --git a/docs/search_index.json b/docs/search_index.json
index 8644d67..c5e4816 100644
--- a/docs/search_index.json
+++ b/docs/search_index.json
@@ -1 +1 @@
-[["index.html", "AnVIL CoFests! 2024 What are CoFests!? What’s in a name: CollaborationFests! and Hackathons AnVIL Collection", " AnVIL CoFests! 2024 September 18, 2024 What are CoFests!? CollaborationFests!, also known as CoFests! (and sometimes as “hackathons”), are collaborative work events where we expand and improve the AnVIL community and the AnVIL ecosystem. Sometimes these gatherings are focused on AnVIL, and sometimes they are part of larger communities. Modified from https://galaxyproject.org/events/cofests What’s in a name: CollaborationFests! and Hackathons We collaborate. AnVIL collaborative events are emphatically called CollaborationFests! rather than Hackathons. Putting Collaboration in the name emphasizes what the events are about for us, and Fest communicates that they are fun events (which they are). “Hackathon” implies an emphasis on code. CoFests! are about contributing and learning how to contribute to all aspects of AnVIL, including training material, community infrastructure, documentation, unit tests, bug reports, and yes, even code. First and foremost AnVIL CoFests! are about growing the community of future contributors. Idea inspiration from [GCC2024][GCC2018] Reporting inspiration from [BioC2018][BioC2020][BioC2023] AnVIL Collection Please check out our full collection of AnVIL and related resources: https://hutchdatascience.org/AnVIL_Collection/ "],["organizer-guide.html", "Organizer Guide CoFests! Goals Logistics Final Product / Report Out Example Schedule for a Track", " Organizer Guide The inaugural AnVIL Community Conference (ACC) 2024 will take place on November 12-13, 2024 in Cold Spring Harbor, NY, immediately before the sixth meeting on Biological Data Science. Overall, ACC is a key event for professionals in the genomics community interested in biomedical and genomic cloud computing and features keynotes, town halls, CoFests! and other such component events. CoFests! provide attendees the opportunity to get some hands-on experience with AnVIL and foster connections within the AnVIL community. CoFests! Goals Build an inclusive community that is supportive of newcomers Collaborate and contribute to open science Produce a final product that accomplishes one of the following for a topic Makes useful forward progress Identifies opportunities and boundaries or limitations Logistics 3 Parallel tracks, 5+ hours across Nov 12/13 Scalable Machine Learning and Data Science Polygenic Risk Score Analysis Wrap a Tool (+ Intro AnVIL/WDL) Scientific Lead and AnVIL Outreach co-Lead for support We expect 4-10 participants per track Prior to the CoFests, the scientific and AnVIL Outreach co-Leads will work together to enumerate some ideas for final products and post them publicly in this book. The AnVIL Outreach co-Lead will help add content to this guide, onboard newer AnVIL users to the platform, and provide guidance on the final product / report out. Final Product / Report Out The final product of CoFests doesn’t need to be code! These Collaboration Fests can support story-boarding future work or development of documentation or training materials. If it’s something that will help the community and make progress on an AnVIL associated topic and there’s sufficient interest, the idea is game! As Galaxy phrased it for their CoFests: [The goal of collaboration fests is to expand the ecosystem] Not just the code, but the whole ecosystem. That includes training, tools, best practice workflows, documentation, test cases, translations, infrastructure, and yes, even code. It helps us a lot if you can fill out some basic Report Out details. At the end of Day 2, your track will share a final report during the CoFest Recap Session! Example Schedule for a Track Day 1 (2.5 hours) Task Time &amp; Lead Problem statement. Provide background info on the track’s overall topic and may include a brief summary of the pre-worked collaboration ideas. 20-30 minutes (Scientific Lead) Brainstorming. What project will the track tackle? Focus on understanding the participant backgrounds and skills and matching those with track ideas and actionable tasks to accomplish the goal. 15-30 minutes (Both) Onboarding. Handle billing accounts and other logistics necessary to accomplish the work. 30-60 minutes (AnVIL Outreach co-Lead) Work-regroup, work-regroup. Formal collaboration work time left before dinner. (Groups may choose to work together informally after dinner too) 30-60 minutes (N/A) Day 2 (3 hours) Task Time &amp; Lead Work-regroup, work-regroup. Formal collaboration work time (with a coffee break). 2-2.5 hours (N/A) Construct a “report out”. The report out may be a Google doc, Google slides, a GitHub repository, a website, an OTTR book, etc. 30-60 minutes (AnVIL Outreach co-Lead) "],["scalable-ml-and-data-science.html", "Chapter 1 Scalable ML and Data Science", " Chapter 1 Scalable ML and Data Science "],["polygenic-risk-score-analysis.html", "Chapter 2 Polygenic Risk Score Analysis", " Chapter 2 Polygenic Risk Score Analysis "],["wrap-a-tool-with-wdl.html", "Chapter 3 Wrap a Tool with WDL", " Chapter 3 Wrap a Tool with WDL "],["about-the-authors.html", "About the Authors", " About the Authors These credits are based on our course contributors table guidelines.     Credits Names Pedagogy Lead Content Instructor(s) FirstName LastName Lecturer(s) (include chapter name/link in parentheses if only for specific chapters) - make new line if more than one chapter involved Delivered the course in some way - video or audio Content Author(s) (include chapter name/link in parentheses if only for specific chapters) - make new line if more than one chapter involved If any other authors besides lead instructor Content Contributor(s) (include section name/link in parentheses) - make new line if more than one section involved Wrote less than a chapter AnVIL instructions: Katherine Cox, Ava Hoffman, Elizabeth Humphries Content Editor(s)/Reviewer(s) Checked your content Content Director(s) Helped guide the content direction Content Consultants (include chapter name/link in parentheses or word “General”) - make new line if more than one chapter involved Gave high level advice on content AnVIL instructions: Allie Cliffe Acknowledgments Gave small assistance to content but not to the level of consulting Production Content Publisher(s) Helped with publishing platform Content Publishing Reviewer(s) Reviewed overall content and aesthetics on publishing platform Technical Course Publishing Engineer(s) Helped with the code for the technical aspects related to the specific course generation Template Publishing Engineers Candace Savonen, Carrie Wright Publishing Maintenance Engineer Candace Savonen Technical Publishing Stylists Carrie Wright, Candace Savonen Package Developers (ottrpal) John Muschelli, Candace Savonen, Carrie Wright Art and Design Illustrator(s) Created graphics for the course Figure Artist(s) Created figures/plots for course Videographer(s) Filmed videos Videography Editor(s) Edited film Audiographer(s) Recorded audio Audiography Editor(s) Edited audio recordings Funding Funder(s) Institution/individual who funded course including grant number Funding Staff Staff members who help with funding   ## ─ Session info ─────────────────────────────────────────────────────────────── ## setting value ## version R version 4.3.2 (2023-10-31) ## os Ubuntu 22.04.4 LTS ## system x86_64, linux-gnu ## ui X11 ## language (EN) ## collate en_US.UTF-8 ## ctype en_US.UTF-8 ## tz Etc/UTC ## date 2024-09-18 ## pandoc 3.1.1 @ /usr/local/bin/ (via rmarkdown) ## ## ─ Packages ─────────────────────────────────────────────────────────────────── ## package * version date (UTC) lib source ## bookdown 0.39.1 2024-06-11 [1] Github (rstudio/bookdown@f244cf1) ## bslib 0.6.1 2023-11-28 [1] RSPM (R 4.3.0) ## cachem 1.0.8 2023-05-01 [1] RSPM (R 4.3.0) ## cli 3.6.2 2023-12-11 [1] RSPM (R 4.3.0) ## devtools 2.4.5 2022-10-11 [1] RSPM (R 4.3.0) ## digest 0.6.34 2024-01-11 [1] RSPM (R 4.3.0) ## ellipsis 0.3.2 2021-04-29 [1] RSPM (R 4.3.0) ## evaluate 0.23 2023-11-01 [1] RSPM (R 4.3.0) ## fastmap 1.1.1 2023-02-24 [1] RSPM (R 4.3.0) ## fs 1.6.3 2023-07-20 [1] RSPM (R 4.3.0) ## glue 1.7.0 2024-01-09 [1] RSPM (R 4.3.0) ## htmltools 0.5.7 2023-11-03 [1] RSPM (R 4.3.0) ## htmlwidgets 1.6.4 2023-12-06 [1] RSPM (R 4.3.0) ## httpuv 1.6.14 2024-01-26 [1] RSPM (R 4.3.0) ## jquerylib 0.1.4 2021-04-26 [1] RSPM (R 4.3.0) ## jsonlite 1.8.8 2023-12-04 [1] RSPM (R 4.3.0) ## knitr 1.47.3 2024-06-11 [1] Github (yihui/knitr@e1edd34) ## later 1.3.2 2023-12-06 [1] RSPM (R 4.3.0) ## lifecycle 1.0.4 2023-11-07 [1] RSPM (R 4.3.0) ## magrittr 2.0.3 2022-03-30 [1] RSPM (R 4.3.0) ## memoise 2.0.1 2021-11-26 [1] RSPM (R 4.3.0) ## mime 0.12 2021-09-28 [1] RSPM (R 4.3.0) ## miniUI 0.1.1.1 2018-05-18 [1] RSPM (R 4.3.0) ## pkgbuild 1.4.3 2023-12-10 [1] RSPM (R 4.3.0) ## pkgload 1.3.4 2024-01-16 [1] RSPM (R 4.3.0) ## profvis 0.3.8 2023-05-02 [1] RSPM (R 4.3.0) ## promises 1.2.1 2023-08-10 [1] RSPM (R 4.3.0) ## purrr 1.0.2 2023-08-10 [1] RSPM (R 4.3.0) ## R6 2.5.1 2021-08-19 [1] RSPM (R 4.3.0) ## Rcpp 1.0.12 2024-01-09 [1] RSPM (R 4.3.0) ## remotes 2.4.2.1 2023-07-18 [1] RSPM (R 4.3.0) ## rlang 1.1.4 2024-06-04 [1] CRAN (R 4.3.2) ## rmarkdown 2.27.1 2024-06-11 [1] Github (rstudio/rmarkdown@e1c93a9) ## sass 0.4.8 2023-12-06 [1] RSPM (R 4.3.0) ## sessioninfo 1.2.2 2021-12-06 [1] RSPM (R 4.3.0) ## shiny 1.8.0 2023-11-17 [1] RSPM (R 4.3.0) ## stringi 1.8.3 2023-12-11 [1] RSPM (R 4.3.0) ## stringr 1.5.1 2023-11-14 [1] RSPM (R 4.3.0) ## urlchecker 1.0.1 2021-11-30 [1] RSPM (R 4.3.0) ## usethis 2.2.3 2024-02-19 [1] RSPM (R 4.3.0) ## vctrs 0.6.5 2023-12-01 [1] RSPM (R 4.3.0) ## xfun 0.44.4 2024-06-11 [1] Github (yihui/xfun@9da62cc) ## xtable 1.8-4 2019-04-21 [1] RSPM (R 4.3.0) ## yaml 2.3.8 2023-12-11 [1] RSPM (R 4.3.0) ## ## [1] /usr/local/lib/R/site-library ## [2] /usr/local/lib/R/library ## ## ────────────────────────────────────────────────────────────────────────────── "],["references.html", "Chapter 4 References", " Chapter 4 References "],["404.html", "Page not found", " Page not found The page you requested cannot be found (perhaps it was moved or renamed). You may want to try searching to find the page's new location, or use the table of contents to find the page you are looking for. "]]
+[["index.html", "AnVIL CoFests! 2024 What are CoFests!? What’s in a name: CollaborationFests! and Hackathons AnVIL Collection", " AnVIL CoFests! 2024 September 24, 2024 What are CoFests!? CollaborationFests!, also known as CoFests! (and sometimes as “hackathons”), are collaborative work events where we expand and improve the AnVIL community and the AnVIL ecosystem. Sometimes these gatherings are focused on AnVIL, and sometimes they are part of larger communities. Modified from https://galaxyproject.org/events/cofests What’s in a name: CollaborationFests! and Hackathons We collaborate. AnVIL collaborative events are emphatically called CollaborationFests! rather than Hackathons. Putting Collaboration in the name emphasizes what the events are about for us, and Fest communicates that they are fun events (which they are). “Hackathon” implies an emphasis on code. CoFests! are about contributing and learning how to contribute to all aspects of AnVIL, including training material, community infrastructure, documentation, unit tests, bug reports, and yes, even code. First and foremost AnVIL CoFests! are about growing the community of future contributors. Idea inspiration from [GCC2024][GCC2018] Reporting inspiration from [BioC2018][BioC2020][BioC2023] AnVIL Collection Please check out our full collection of AnVIL and related resources: https://hutchdatascience.org/AnVIL_Collection/ "],["organizer-guide.html", "Organizer Guide CoFests! Goals Logistics Final Product / Report Out Example Schedule for a Track", " Organizer Guide The inaugural AnVIL Community Conference (ACC) 2024 will take place on November 12-13, 2024 in Cold Spring Harbor, NY, immediately before the sixth meeting on Biological Data Science. Overall, ACC is a key event for professionals in the genomics community interested in biomedical and genomic cloud computing and features keynotes, town halls, CoFests! and other such component events. CoFests! provide attendees the opportunity to get some hands-on experience with AnVIL and foster connections within the AnVIL community. CoFests! Goals Build an inclusive community that is supportive of newcomers Collaborate and contribute to open science Produce a final product that accomplishes one of the following for a topic Makes useful forward progress Identifies opportunities and boundaries or limitations Logistics 3 Parallel tracks, 5+ hours across Nov 12/13 Scalable Machine Learning and Data Science Polygenic Risk Score Analysis Wrap a Tool (+ Intro AnVIL/WDL) Scientific Lead and AnVIL Outreach co-Lead for support We expect 4-10 participants per track Prior to the CoFests, the scientific and AnVIL Outreach co-Leads will work together to enumerate some ideas for final products and post them publicly in this book. The AnVIL Outreach co-Lead will help add content to this guide, onboard newer AnVIL users to the platform, and provide guidance on the final product / report out. Final Product / Report Out The final product of CoFests doesn’t need to be code! These Collaboration Fests can support story-boarding future work or development of documentation or training materials. If it’s something that will help the community and make progress on an AnVIL associated topic and there’s sufficient interest, the idea is game! As Galaxy phrased it for their CoFests: [The goal of collaboration fests is to expand the ecosystem] Not just the code, but the whole ecosystem. That includes training, tools, best practice workflows, documentation, test cases, translations, infrastructure, and yes, even code. It helps us a lot if you can fill out some basic Report Out details. At the end of Day 2, your track will share a final report during the CoFest Recap Session! Example Schedule for a Track Day 1 (2.5 hours) Task Time &amp; Lead Problem statement. Provide background info on the track’s overall topic and may include a brief summary of the pre-worked collaboration ideas. 20-30 minutes (Scientific Lead) Brainstorming. What project will the track tackle? Focus on understanding the participant backgrounds and skills and matching those with track ideas and actionable tasks to accomplish the goal. 15-30 minutes (Both) Onboarding. Handle billing accounts and other logistics necessary to accomplish the work. 30-60 minutes (AnVIL Outreach co-Lead) Work-regroup, work-regroup. Formal collaboration work time left before dinner. (Groups may choose to work together informally after dinner too) 30-60 minutes (N/A) Day 2 (3 hours) Task Time &amp; Lead Work-regroup, work-regroup. Formal collaboration work time (with a coffee break). 2-2.5 hours (N/A) Construct a “report out”. The report out may be a Google doc, Google slides, a GitHub repository, a website, an OTTR book, etc. 30-60 minutes (AnVIL Outreach co-Lead) "],["scalable-ml-and-data-science.html", "Chapter 1 Scalable ML and Data Science", " Chapter 1 Scalable ML and Data Science "],["polygenic-risk-score-analysis.html", "Chapter 2 Polygenic Risk Score Analysis", " Chapter 2 Polygenic Risk Score Analysis "],["how-to-run-your-tool-in-anvil-with-wdl.html", "Chapter 3 How to Run Your Tool in AnVIL with WDL", " Chapter 3 How to Run Your Tool in AnVIL with WDL "],["about-the-authors.html", "About the Authors", " About the Authors These credits are based on our course contributors table guidelines.     Credits Names Pedagogy Lead Content Instructor(s) FirstName LastName Lecturer(s) (include chapter name/link in parentheses if only for specific chapters) - make new line if more than one chapter involved Delivered the course in some way - video or audio Content Author(s) (include chapter name/link in parentheses if only for specific chapters) - make new line if more than one chapter involved If any other authors besides lead instructor Content Contributor(s) (include section name/link in parentheses) - make new line if more than one section involved Wrote less than a chapter AnVIL instructions: Katherine Cox, Ava Hoffman, Elizabeth Humphries Content Editor(s)/Reviewer(s) Checked your content Content Director(s) Helped guide the content direction Content Consultants (include chapter name/link in parentheses or word “General”) - make new line if more than one chapter involved Gave high level advice on content AnVIL instructions: Allie Cliffe Acknowledgments Gave small assistance to content but not to the level of consulting Production Content Publisher(s) Helped with publishing platform Content Publishing Reviewer(s) Reviewed overall content and aesthetics on publishing platform Technical Course Publishing Engineer(s) Helped with the code for the technical aspects related to the specific course generation Template Publishing Engineers Candace Savonen, Carrie Wright Publishing Maintenance Engineer Candace Savonen Technical Publishing Stylists Carrie Wright, Candace Savonen Package Developers (ottrpal) John Muschelli, Candace Savonen, Carrie Wright Art and Design Illustrator(s) Created graphics for the course Figure Artist(s) Created figures/plots for course Videographer(s) Filmed videos Videography Editor(s) Edited film Audiographer(s) Recorded audio Audiography Editor(s) Edited audio recordings Funding Funder(s) Institution/individual who funded course including grant number Funding Staff Staff members who help with funding   ## ─ Session info ─────────────────────────────────────────────────────────────── ## setting value ## version R version 4.3.2 (2023-10-31) ## os Ubuntu 22.04.4 LTS ## system x86_64, linux-gnu ## ui X11 ## language (EN) ## collate en_US.UTF-8 ## ctype en_US.UTF-8 ## tz Etc/UTC ## date 2024-09-24 ## pandoc 3.1.1 @ /usr/local/bin/ (via rmarkdown) ## ## ─ Packages ─────────────────────────────────────────────────────────────────── ## package * version date (UTC) lib source ## bookdown 0.39.1 2024-06-11 [1] Github (rstudio/bookdown@f244cf1) ## bslib 0.6.1 2023-11-28 [1] RSPM (R 4.3.0) ## cachem 1.0.8 2023-05-01 [1] RSPM (R 4.3.0) ## cli 3.6.2 2023-12-11 [1] RSPM (R 4.3.0) ## devtools 2.4.5 2022-10-11 [1] RSPM (R 4.3.0) ## digest 0.6.34 2024-01-11 [1] RSPM (R 4.3.0) ## ellipsis 0.3.2 2021-04-29 [1] RSPM (R 4.3.0) ## evaluate 0.23 2023-11-01 [1] RSPM (R 4.3.0) ## fastmap 1.1.1 2023-02-24 [1] RSPM (R 4.3.0) ## fs 1.6.3 2023-07-20 [1] RSPM (R 4.3.0) ## glue 1.7.0 2024-01-09 [1] RSPM (R 4.3.0) ## htmltools 0.5.7 2023-11-03 [1] RSPM (R 4.3.0) ## htmlwidgets 1.6.4 2023-12-06 [1] RSPM (R 4.3.0) ## httpuv 1.6.14 2024-01-26 [1] RSPM (R 4.3.0) ## jquerylib 0.1.4 2021-04-26 [1] RSPM (R 4.3.0) ## jsonlite 1.8.8 2023-12-04 [1] RSPM (R 4.3.0) ## knitr 1.47.3 2024-06-11 [1] Github (yihui/knitr@e1edd34) ## later 1.3.2 2023-12-06 [1] RSPM (R 4.3.0) ## lifecycle 1.0.4 2023-11-07 [1] RSPM (R 4.3.0) ## magrittr 2.0.3 2022-03-30 [1] RSPM (R 4.3.0) ## memoise 2.0.1 2021-11-26 [1] RSPM (R 4.3.0) ## mime 0.12 2021-09-28 [1] RSPM (R 4.3.0) ## miniUI 0.1.1.1 2018-05-18 [1] RSPM (R 4.3.0) ## pkgbuild 1.4.3 2023-12-10 [1] RSPM (R 4.3.0) ## pkgload 1.3.4 2024-01-16 [1] RSPM (R 4.3.0) ## profvis 0.3.8 2023-05-02 [1] RSPM (R 4.3.0) ## promises 1.2.1 2023-08-10 [1] RSPM (R 4.3.0) ## purrr 1.0.2 2023-08-10 [1] RSPM (R 4.3.0) ## R6 2.5.1 2021-08-19 [1] RSPM (R 4.3.0) ## Rcpp 1.0.12 2024-01-09 [1] RSPM (R 4.3.0) ## remotes 2.4.2.1 2023-07-18 [1] RSPM (R 4.3.0) ## rlang 1.1.4 2024-06-04 [1] CRAN (R 4.3.2) ## rmarkdown 2.27.1 2024-06-11 [1] Github (rstudio/rmarkdown@e1c93a9) ## sass 0.4.8 2023-12-06 [1] RSPM (R 4.3.0) ## sessioninfo 1.2.2 2021-12-06 [1] RSPM (R 4.3.0) ## shiny 1.8.0 2023-11-17 [1] RSPM (R 4.3.0) ## stringi 1.8.3 2023-12-11 [1] RSPM (R 4.3.0) ## stringr 1.5.1 2023-11-14 [1] RSPM (R 4.3.0) ## urlchecker 1.0.1 2021-11-30 [1] RSPM (R 4.3.0) ## usethis 2.2.3 2024-02-19 [1] RSPM (R 4.3.0) ## vctrs 0.6.5 2023-12-01 [1] RSPM (R 4.3.0) ## xfun 0.44.4 2024-06-11 [1] Github (yihui/xfun@9da62cc) ## xtable 1.8-4 2019-04-21 [1] RSPM (R 4.3.0) ## yaml 2.3.8 2023-12-11 [1] RSPM (R 4.3.0) ## ## [1] /usr/local/lib/R/site-library ## [2] /usr/local/lib/R/library ## ## ────────────────────────────────────────────────────────────────────────────── "],["references.html", "Chapter 4 References", " Chapter 4 References "],["404.html", "Page not found", " Page not found The page you requested cannot be found (perhaps it was moved or renamed). You may want to try searching to find the page's new location, or use the table of contents to find the page you are looking for. "]]
diff --git a/docs/wrap-tool.md b/docs/wrap-tool.md
index d65db0c..d8d1b6c 100644
--- a/docs/wrap-tool.md
+++ b/docs/wrap-tool.md
@@ -1 +1 @@
-# Wrap a Tool with WDL
+# How to Run Your Tool in AnVIL with WDL