diff --git a/404.html b/404.html
index a3c6926..fcf5ce8 100644
--- a/404.html
+++ b/404.html
@@ -74,7 +74,7 @@
 
     <footer><div class="pkgdown-footer-left">
   <p></p>
-<p>Developed by Amy Paguirigan.</p>
+<p>Developed by Amy Paguirigan, Scott Chamberlain.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html
new file mode 100644
index 0000000..6c7f145
--- /dev/null
+++ b/CODE_OF_CONDUCT.html
@@ -0,0 +1,137 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Contributor Covenant Code of Conduct • rcromwell</title><script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="Contributor Covenant Code of Conduct"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]--></head><body>
+    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
+    
+
+    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    
+    <a class="navbar-brand me-2" href="index.html">rcromwell</a>
+
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0</small>
+
+    
+    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
+      <span class="navbar-toggler-icon"></span>
+    </button>
+
+    <div id="navbar" class="collapse navbar-collapse ms-3">
+      <ul class="navbar-nav me-auto"><li class="nav-item">
+  <a class="nav-link" href="articles/rcromwell.html">Get started</a>
+</li>
+<li class="nav-item">
+  <a class="nav-link" href="reference/index.html">Reference</a>
+</li>
+<li class="nav-item">
+  <a class="nav-link" href="news/index.html">Changelog</a>
+</li>
+      </ul><form class="form-inline my-2 my-lg-0" role="search">
+        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
+
+      <ul class="navbar-nav"><li class="nav-item">
+  <a class="external-link nav-link" href="https://github.com/getwilds/rcromwell/" aria-label="github">
+    <span class="fab fa fab fa-github fa-lg"></span>
+     
+  </a>
+</li>
+      </ul></div>
+
+    
+  </div>
+</nav><div class="container template-title-body">
+<div class="row">
+  <main id="main" class="col-md-9"><div class="page-header">
+      <img src="" class="logo" alt=""><h1>Contributor Covenant Code of Conduct</h1>
+      <small class="dont-index">Source: <a href="https://github.com/getwilds/rcromwell/blob/HEAD/.github/CODE_OF_CONDUCT.md" class="external-link"><code>.github/CODE_OF_CONDUCT.md</code></a></small>
+    </div>
+
+<div id="contributor-covenant-code-of-conduct" class="section level1">
+
+<div class="section level2">
+<h2 id="our-pledge">Our Pledge<a class="anchor" aria-label="anchor" href="#our-pledge"></a></h2>
+<p>We as members, contributors, and leaders pledge to make participation in our community a harassment-free experience for everyone, regardless of age, body size, visible or invisible disability, ethnicity, sex characteristics, gender identity and expression, level of experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, or sexual identity and orientation.</p>
+<p>We pledge to act and interact in ways that contribute to an open, welcoming, diverse, inclusive, and healthy community.</p>
+</div>
+<div class="section level2">
+<h2 id="our-standards">Our Standards<a class="anchor" aria-label="anchor" href="#our-standards"></a></h2>
+<p>Examples of behavior that contributes to a positive environment for our community include:</p>
+<ul><li>Demonstrating empathy and kindness toward other people</li>
+<li>Being respectful of differing opinions, viewpoints, and experiences</li>
+<li>Giving and gracefully accepting constructive feedback</li>
+<li>Accepting responsibility and apologizing to those affected by our mistakes, and learning from the experience</li>
+<li>Focusing on what is best not just for us as individuals, but for the overall community</li>
+</ul><p>Examples of unacceptable behavior include:</p>
+<ul><li>The use of sexualized language or imagery, and sexual attention or advances of any kind</li>
+<li>Trolling, insulting or derogatory comments, and personal or political attacks</li>
+<li>Public or private harassment</li>
+<li>Publishing others’ private information, such as a physical or email address, without their explicit permission</li>
+<li>Other conduct which could reasonably be considered inappropriate in a professional setting</li>
+</ul></div>
+<div class="section level2">
+<h2 id="enforcement-responsibilities">Enforcement Responsibilities<a class="anchor" aria-label="anchor" href="#enforcement-responsibilities"></a></h2>
+<p>Community leaders are responsible for clarifying and enforcing our standards of acceptable behavior and will take appropriate and fair corrective action in response to any behavior that they deem inappropriate, threatening, offensive, or harmful.</p>
+<p>Community leaders have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, and will communicate reasons for moderation decisions when appropriate.</p>
+</div>
+<div class="section level2">
+<h2 id="scope">Scope<a class="anchor" aria-label="anchor" href="#scope"></a></h2>
+<p>This Code of Conduct applies within all community spaces, and also applies when an individual is officially representing the community in public spaces. Examples of representing our community include using an official e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event.</p>
+</div>
+<div class="section level2">
+<h2 id="enforcement">Enforcement<a class="anchor" aria-label="anchor" href="#enforcement"></a></h2>
+<p>Instances of abusive, harassing, or otherwise unacceptable behavior may be reported to the community leaders responsible for enforcement at <a href="mailto:sachamber@fredhutch.org" class="email">sachamber@fredhutch.org</a>. All complaints will be reviewed and investigated promptly and fairly.</p>
+<p>All community leaders are obligated to respect the privacy and security of the reporter of any incident.</p>
+</div>
+<div class="section level2">
+<h2 id="enforcement-guidelines">Enforcement Guidelines<a class="anchor" aria-label="anchor" href="#enforcement-guidelines"></a></h2>
+<p>Community leaders will follow these Community Impact Guidelines in determining the consequences for any action they deem in violation of this Code of Conduct:</p>
+<div class="section level3">
+<h3 id="id_1-correction">1. Correction<a class="anchor" aria-label="anchor" href="#id_1-correction"></a></h3>
+<p><strong>Community Impact</strong>: Use of inappropriate language or other behavior deemed unprofessional or unwelcome in the community.</p>
+<p><strong>Consequence</strong>: A private, written warning from community leaders, providing clarity around the nature of the violation and an explanation of why the behavior was inappropriate. A public apology may be requested.</p>
+</div>
+<div class="section level3">
+<h3 id="id_2-warning">2. Warning<a class="anchor" aria-label="anchor" href="#id_2-warning"></a></h3>
+<p><strong>Community Impact</strong>: A violation through a single incident or series of actions.</p>
+<p><strong>Consequence</strong>: A warning with consequences for continued behavior. No interaction with the people involved, including unsolicited interaction with those enforcing the Code of Conduct, for a specified period of time. This includes avoiding interactions in community spaces as well as external channels like social media. Violating these terms may lead to a temporary or permanent ban.</p>
+</div>
+<div class="section level3">
+<h3 id="id_3-temporary-ban">3. Temporary Ban<a class="anchor" aria-label="anchor" href="#id_3-temporary-ban"></a></h3>
+<p><strong>Community Impact</strong>: A serious violation of community standards, including sustained inappropriate behavior.</p>
+<p><strong>Consequence</strong>: A temporary ban from any sort of interaction or public communication with the community for a specified period of time. No public or private interaction with the people involved, including unsolicited interaction with those enforcing the Code of Conduct, is allowed during this period. Violating these terms may lead to a permanent ban.</p>
+</div>
+<div class="section level3">
+<h3 id="id_4-permanent-ban">4. Permanent Ban<a class="anchor" aria-label="anchor" href="#id_4-permanent-ban"></a></h3>
+<p><strong>Community Impact</strong>: Demonstrating a pattern of violation of community standards, including sustained inappropriate behavior, harassment of an individual, or aggression toward or disparagement of classes of individuals.</p>
+<p><strong>Consequence</strong>: A permanent ban from any sort of public interaction within the community.</p>
+</div>
+</div>
+<div class="section level2">
+<h2 id="attribution">Attribution<a class="anchor" aria-label="anchor" href="#attribution"></a></h2>
+<p>This Code of Conduct is adapted from the <a href="https://www.contributor-covenant.org" class="external-link">Contributor Covenant</a>, version 2.1, available at <a href="https://www.contributor-covenant.org/version/2/1/code_of_conduct.html" class="external-link uri">https://www.contributor-covenant.org/version/2/1/code_of_conduct.html</a>.</p>
+<p>Community Impact Guidelines were inspired by [Mozilla’s code of conduct enforcement ladder][<a href="https://github.com/mozilla/inclusion" class="external-link uri">https://github.com/mozilla/inclusion</a>].</p>
+<p>For answers to common questions about this code of conduct, see the FAQ at <a href="https://www.contributor-covenant.org/faq" class="external-link uri">https://www.contributor-covenant.org/faq</a>. Translations are available at <a href="https://www.contributor-covenant.org/translations" class="external-link uri">https://www.contributor-covenant.org/translations</a>.</p>
+</div>
+</div>
+
+  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
+    </nav></aside></div>
+
+
+    <footer><div class="pkgdown-footer-left">
+  <p></p><p>Developed by Amy Paguirigan, Scott Chamberlain.</p>
+</div>
+
+<div class="pkgdown-footer-right">
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
+</div>
+
+    </footer></div>
+
+  
+
+  
+
+  </body></html>
+
diff --git a/LICENSE-text.html b/LICENSE-text.html
index 0f38360..d2fff2e 100644
--- a/LICENSE-text.html
+++ b/LICENSE-text.html
@@ -55,7 +55,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Amy Paguirigan.</p>
+  <p></p><p>Developed by Amy Paguirigan, Scott Chamberlain.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/LICENSE.html b/LICENSE.html
index e5c9d4e..4538584 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -59,7 +59,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Amy Paguirigan.</p>
+  <p></p><p>Developed by Amy Paguirigan, Scott Chamberlain.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/articles/index.html b/articles/index.html
index f4b976f..56faaf7 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -57,7 +57,7 @@ <h3>All vignettes</h3>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Amy Paguirigan.</p>
+  <p></p><p>Developed by Amy Paguirigan, Scott Chamberlain.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/articles/rcromwell.html b/articles/rcromwell.html
index 4934fa5..42ee328 100644
--- a/articles/rcromwell.html
+++ b/articles/rcromwell.html
@@ -183,7 +183,7 @@ <h2 id="now-get-all-your-metadata-and-track-the-workflow">Now get all your metad
 
     <footer><div class="pkgdown-footer-left">
   <p></p>
-<p>Developed by Amy Paguirigan.</p>
+<p>Developed by Amy Paguirigan, Scott Chamberlain.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/authors.html b/authors.html
index b1f6000..8a17d26 100644
--- a/authors.html
+++ b/authors.html
@@ -50,7 +50,11 @@
       <h2>Authors</h2>
       
       <ul class="list-unstyled"><li>
-          <p><strong>Amy Paguirigan</strong>. Author, maintainer. <a href="https://orcid.org/0000-0002-6819-9736" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
+          <p><strong>Amy Paguirigan</strong>. Author. <a href="https://orcid.org/0000-0002-6819-9736" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
+          </p>
+        </li>
+        <li>
+          <p><strong>Scott Chamberlain</strong>. Author, maintainer. <a href="https://orcid.org/0000-0003-1444-9135" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
           </p>
         </li>
       </ul></div>
@@ -59,14 +63,14 @@ <h2>Authors</h2>
       <h2 id="citation">Citation</h2>
       <p><small class="dont-index">Source: <a href="https://github.com/getwilds/rcromwell/blob/HEAD/DESCRIPTION" class="external-link"><code>DESCRIPTION</code></a></small></p>
 
-      <p>Paguirigan A (2024).
+      <p>Paguirigan A, Chamberlain S (2024).
 <em>rcromwell: Convenience Tools for Managing WDL Workflows via Cromwell</em>.
 R package version 3.0.0http://getwilds.org/rcromwell/ (website)
 https://github.com/getwilds/rcromwell (devel), <a href="http://getwilds.org/rcromwell/%20(website)https://github.com/getwilds/rcromwell%20(devel)">http://getwilds.org/rcromwell/ (website)https://github.com/getwilds/rcromwell (devel)</a>. 
 </p>
       <pre>@Manual{,
   title = {rcromwell: Convenience Tools for Managing WDL Workflows via Cromwell},
-  author = {Amy Paguirigan},
+  author = {Amy Paguirigan and Scott Chamberlain},
   year = {2024},
   note = {R package version 3.0.0http://getwilds.org/rcromwell/ (website)
 https://github.com/getwilds/rcromwell (devel)},
@@ -79,7 +83,7 @@ <h2 id="citation">Citation</h2>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Amy Paguirigan.</p>
+  <p></p><p>Developed by Amy Paguirigan, Scott Chamberlain.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/index.html b/index.html
index 79c8aca..8cfae28 100644
--- a/index.html
+++ b/index.html
@@ -69,6 +69,8 @@
 <!-- badges: start -->
 
 <p>Convenience Tools for Managing WDL Workflows via Cromwell</p>
+<p>Cromwell is a scientific workflow engine designed for simplicity and scalability. It’s maintained by the <a href="https://www.broadinstitute.org/" class="external-link">Broad Institute</a>. (<a href="https://cromwell.readthedocs.io/en/latest/" class="external-link">docs</a>, <a href="https://github.com/broadinstitute/cromwell" class="external-link">code source</a>).</p>
+<p><code>rcromwell</code> is maintained by the <a href="https://hutchdatascience.org/" class="external-link">Fred Hutch Cancer Center Data Science Lab</a>.</p>
 <div class="section level2">
 <h2 id="installation">Installation<a class="anchor" aria-label="anchor" href="#installation"></a>
 </h2>
@@ -78,85 +80,27 @@ <h2 id="installation">Installation<a class="anchor" aria-label="anchor" href="#i
 <span><span class="fu">pak</span><span class="fu">::</span><span class="fu"><a href="https://pak.r-lib.org/reference/pak.html" class="external-link">pak</a></span><span class="op">(</span><span class="st">"getwilds/rcromwell"</span><span class="op">)</span></span></code></pre></div>
 <p>Install a specific release version (in this case v1.0) by:</p>
 <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="fu">pak</span><span class="fu">::</span><span class="fu"><a href="https://pak.r-lib.org/reference/pak.html" class="external-link">pak</a></span><span class="op">(</span><span class="st">'getwilds/rcromwell@v1.0'</span><span class="op">)</span></span></code></pre></div>
+<code class="sourceCode R"><span><span class="fu">pak</span><span class="fu">::</span><span class="fu"><a href="https://pak.r-lib.org/reference/pak.html" class="external-link">pak</a></span><span class="op">(</span><span class="st">'getwilds/rcromwell@v1.1.0'</span><span class="op">)</span></span></code></pre></div>
 </div>
 <div class="section level2">
-<h2 id="example-workflow-process">Example workflow process<a class="anchor" aria-label="anchor" href="#example-workflow-process"></a>
+<h2 id="documentation">Documentation<a class="anchor" aria-label="anchor" href="#documentation"></a>
 </h2>
-<p>Set your Cromwell URL</p>
-<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="http://getwilds.org/rcromwell/">rcromwell</a></span><span class="op">)</span></span>
-<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span>
-<span><span class="fu"><a href="reference/cromwell_config.html">cromwell_config</a></span><span class="op">(</span><span class="st">"http://localhost:20202"</span><span class="op">)</span></span></code></pre></div>
-<div class="section level3">
-<h3 id="validate-your-workflow-formatting">Validate your workflow formatting<a class="anchor" aria-label="anchor" href="#validate-your-workflow-formatting"></a>
-</h3>
-<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/list.files.html" class="external-link">list.files</a></span><span class="op">(</span>pattern <span class="op">=</span> <span class="st">"*.wdl"</span><span class="op">)</span></span>
-<span><span class="va">valid</span> <span class="op">&lt;-</span> <span class="fu"><a href="reference/cromwell_validate.html">cromwell_validate</a></span><span class="op">(</span>wdl <span class="op">=</span> <span class="st">"myworkflow.wdl"</span><span class="op">)</span></span>
-<span><span class="va">valid</span><span class="op">[[</span><span class="st">"errors"</span><span class="op">]</span><span class="op">]</span></span></code></pre></div>
-</div>
-<div class="section level3">
-<h3 id="go-fix-your-issues-now-send-your-workflow-to-crowmell">Go fix your issues, now send your workflow to Crowmell<a class="anchor" aria-label="anchor" href="#go-fix-your-issues-now-send-your-workflow-to-crowmell"></a>
-</h3>
-<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="va">thisJob</span> <span class="op">&lt;-</span> <span class="fu"><a href="reference/cromwell_submit_batch.html">cromwell_submit_batch</a></span><span class="op">(</span>wdl <span class="op">=</span> <span class="st">"myworkflow.wdl"</span>,</span>
-<span>                    params <span class="op">=</span> <span class="st">"myworkflow-parameters.json"</span>,</span>
-<span>                    batch <span class="op">=</span> <span class="st">"myworkflow-batch.json"</span>,</span>
-<span>                    options <span class="op">=</span> <span class="st">"workflow-options.json"</span><span class="op">)</span></span>
-<span><span class="op">(</span><span class="va">thisOne</span> <span class="op">&lt;-</span> <span class="va">thisJob</span><span class="op">$</span><span class="va">id</span><span class="op">)</span></span></code></pre></div>
-<p><code>thisJob$id</code> is the unique Cromwell ID for your entire workflow - you can use that to request all sorts of metadata!!!</p>
-</div>
-<div class="section level3">
-<h3 id="now-get-all-your-metadata-and-track-the-workflow">Now get all your metadata and track the workflow!!<a class="anchor" aria-label="anchor" href="#now-get-all-your-metadata-and-track-the-workflow"></a>
-</h3>
-<p>Return a data frame of all jobs run in the past number of days (uses your database)</p>
-<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="fu"><a href="reference/cromwell_jobs.html">cromwell_jobs</a></span><span class="op">(</span>days <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></code></pre></div>
-<p>Return a data frame (one line if you only submit one workflow id) containing workflow level metadata</p>
-<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="va">w</span> <span class="op">&lt;-</span> <span class="fu"><a href="reference/cromwell_workflow.html">cromwell_workflow</a></span><span class="op">(</span><span class="va">thisOne</span><span class="op">)</span></span></code></pre></div>
-<p>Print the current status of the workflow(s) is(are)</p>
-<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="va">w</span><span class="op">$</span><span class="va">status</span></span></code></pre></div>
-<p>Return a data frame containing all call level metadata</p>
-<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="va">df</span> <span class="op">&lt;-</span> <span class="fu"><a href="reference/cromwell_call.html">cromwell_call</a></span><span class="op">(</span><span class="va">thisOne</span><span class="op">)</span></span></code></pre></div>
-<p>Handy set of dplyr commands to tell you about how the various calls are doing</p>
-<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
-<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">callName</span>, <span class="va">executionStatus</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
-<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarize</a></span><span class="op">(</span>status <span class="op">=</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/context.html" class="external-link">n</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
-<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">executionStatus</span><span class="op">)</span></span></code></pre></div>
-<p>Returns a data frame containing call level call caching metadata</p>
-<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="va">ca</span> <span class="op">&lt;-</span> <span class="fu"><a href="reference/cromwell_cache.html">cromwell_cache</a></span><span class="op">(</span><span class="va">thisOne</span><span class="op">)</span></span></code></pre></div>
-<p>Handy set of dplyr commands to tell you about what sort of call caching is happening</p>
-<div class="sourceCode" id="cb12"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="va">ca</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
-<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">callCaching.hit</span>, <span class="va">callName</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
-<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarize</a></span><span class="op">(</span>hits <span class="op">=</span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/context.html" class="external-link">n</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
-<p>Opens up a popup in your browser with a timing diagram in it.</p>
-<div class="sourceCode" id="cb13"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="fu"><a href="reference/cromwell_timing.html">cromwell_timing</a></span><span class="op">(</span><span class="va">thisOne</span><span class="op">)</span></span></code></pre></div>
-<p>Returns a data frame containing call level failure metadata</p>
-<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="fu"><a href="reference/cromwell_failures.html">cromwell_failures</a></span><span class="op">(</span><span class="va">thisOne</span><span class="op">)</span></span></code></pre></div>
-<p>Will tell Cromwell to abort the current workflow - note this cannot be undone and it will take a while to stop all the jobs.</p>
-<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="fu"><a href="reference/cromwell_abort.html">cromwell_abort</a></span><span class="op">(</span><span class="va">thisOne</span><span class="op">)</span></span></code></pre></div>
-<p>When a workflow is done, request information about the workflow outputs.</p>
-<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="fu"><a href="reference/cromwell_outputs.html">cromwell_outputs</a></span><span class="op">(</span><span class="va">thisOne</span><span class="op">)</span></span></code></pre></div>
-</div>
-<div class="section level3">
-<h3 id="misc-stuff">Misc stuff<a class="anchor" aria-label="anchor" href="#misc-stuff"></a>
-</h3>
-<p>Ugly list of raw metadata should you need it for workflow troubleshooting</p>
-<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="va">wtf</span> <span class="op">&lt;-</span> <span class="fu"><a href="reference/cromwell_glob.html">cromwell_glob</a></span><span class="op">(</span><span class="va">thisOne</span><span class="op">)</span></span>
-<span><span class="va">wtf</span><span class="op">[[</span><span class="st">"failures"</span><span class="op">]</span><span class="op">]</span></span></code></pre></div>
+<p>Go to <a href="http://getwilds.org/rcromwell/" class="uri">http://getwilds.org/rcromwell/</a> for <code>rcromwell</code> package documentation. Go to the <strong>Get Started</strong> vignette to get started!</p>
 </div>
+<div class="section level2">
+<h2 id="bugs-features">Bugs? Features?<a class="anchor" aria-label="anchor" href="#bugs-features"></a>
+</h2>
+<p>Open an issue on our <a href="https://github.com/getwilds/rcromwell/issues/" class="external-link">issue tracker</a>.</p>
+</div>
+<div class="section level2">
+<h2 id="code-of-conduct">Code of Conduct<a class="anchor" aria-label="anchor" href="#code-of-conduct"></a>
+</h2>
+<p>Please note that the rcromwell project is released with a <a href="http://getwilds.org/rcromwell/CODE_OF_CONDUCT.html">Contributor Code of Conduct</a>. By contributing to this project, you agree to abide by its terms.</p>
+</div>
+<div class="section level2">
+<h2 id="license">License<a class="anchor" aria-label="anchor" href="#license"></a>
+</h2>
+<p><a href="LICENSE.html">MIT</a></p>
 </div>
 </div>
   </main><aside class="col-md-3"><div class="links">
@@ -175,6 +119,12 @@ <h2 data-toc-skip>License</h2>
 </ul>
 </div>
 
+<div class="community">
+<h2 data-toc-skip>Community</h2>
+<ul class="list-unstyled">
+<li><a href="CODE_OF_CONDUCT.html">Code of conduct</a></li>
+</ul>
+</div>
 
 <div class="citation">
 <h2 data-toc-skip>Citation</h2>
@@ -186,7 +136,8 @@ <h2 data-toc-skip>Citation</h2>
 <div class="developers">
 <h2 data-toc-skip>Developers</h2>
 <ul class="list-unstyled">
-<li>Amy Paguirigan <br><small class="roles"> Author, maintainer </small> <a href="https://orcid.org/0000-0002-6819-9736" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
+<li>Amy Paguirigan <br><small class="roles"> Author </small> <a href="https://orcid.org/0000-0002-6819-9736" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
+<li>Scott Chamberlain <br><small class="roles"> Author, maintainer </small> <a href="https://orcid.org/0000-0003-1444-9135" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
 </ul>
 </div>
 
@@ -204,7 +155,7 @@ <h2 data-toc-skip>Dev status</h2>
 
     <footer><div class="pkgdown-footer-left">
   <p></p>
-<p>Developed by Amy Paguirigan.</p>
+<p>Developed by Amy Paguirigan, Scott Chamberlain.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/news/index.html b/news/index.html
index ad0e5a7..28fad05 100644
--- a/news/index.html
+++ b/news/index.html
@@ -60,7 +60,7 @@ <h2 class="pkg-version" data-toc-text="3.0.0" id="rcromwell-300">rcromwell 3.0.0
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Amy Paguirigan.</p>
+  <p></p><p>Developed by Amy Paguirigan, Scott Chamberlain.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/pkgdown.yml b/pkgdown.yml
index 21ceaac..d98af6e 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -3,7 +3,7 @@ pkgdown: 2.0.7
 pkgdown_sha: ~
 articles:
   rcromwell: rcromwell.html
-last_built: 2024-01-24T23:02Z
+last_built: 2024-01-31T00:00Z
 urls:
   reference: http://getwilds.org/rcromwell/reference
   article: http://getwilds.org/rcromwell/articles
diff --git a/reference/cromwellSettings.html b/reference/cromwellSettings.html
index f7e3249..dc79465 100644
--- a/reference/cromwellSettings.html
+++ b/reference/cromwellSettings.html
@@ -87,7 +87,7 @@ <h2 id="verbose-messaging">Verbose messaging<a class="anchor" aria-label="anchor
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Amy Paguirigan.</p>
+  <p></p><p>Developed by Amy Paguirigan, Scott Chamberlain.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/cromwell_abort.html b/reference/cromwell_abort.html
index 72e3030..5ad63a3 100644
--- a/reference/cromwell_abort.html
+++ b/reference/cromwell_abort.html
@@ -85,7 +85,7 @@ <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a><
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Amy Paguirigan.</p>
+  <p></p><p>Developed by Amy Paguirigan, Scott Chamberlain.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/cromwell_backends.html b/reference/cromwell_backends.html
index 5329d1a..9fc6aa4 100644
--- a/reference/cromwell_backends.html
+++ b/reference/cromwell_backends.html
@@ -79,7 +79,7 @@ <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a><
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Amy Paguirigan.</p>
+  <p></p><p>Developed by Amy Paguirigan, Scott Chamberlain.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/cromwell_cache.html b/reference/cromwell_cache.html
index eac1dea..d5db7da 100644
--- a/reference/cromwell_cache.html
+++ b/reference/cromwell_cache.html
@@ -86,7 +86,7 @@ <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a><
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Amy Paguirigan.</p>
+  <p></p><p>Developed by Amy Paguirigan, Scott Chamberlain.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/cromwell_call.html b/reference/cromwell_call.html
index ae6979c..2fe816e 100644
--- a/reference/cromwell_call.html
+++ b/reference/cromwell_call.html
@@ -103,7 +103,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Amy Paguirigan.</p>
+  <p></p><p>Developed by Amy Paguirigan, Scott Chamberlain.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/cromwell_config.html b/reference/cromwell_config.html
index 8963dbb..a5f3a7a 100644
--- a/reference/cromwell_config.html
+++ b/reference/cromwell_config.html
@@ -96,7 +96,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Amy Paguirigan.</p>
+  <p></p><p>Developed by Amy Paguirigan, Scott Chamberlain.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/cromwell_failures.html b/reference/cromwell_failures.html
index f36ba1e..63cbe08 100644
--- a/reference/cromwell_failures.html
+++ b/reference/cromwell_failures.html
@@ -99,7 +99,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Amy Paguirigan.</p>
+  <p></p><p>Developed by Amy Paguirigan, Scott Chamberlain.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/cromwell_glob.html b/reference/cromwell_glob.html
index b018a9b..d0566a9 100644
--- a/reference/cromwell_glob.html
+++ b/reference/cromwell_glob.html
@@ -103,7 +103,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Amy Paguirigan.</p>
+  <p></p><p>Developed by Amy Paguirigan, Scott Chamberlain.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/cromwell_jobs.html b/reference/cromwell_jobs.html
index 7e69d65..b323bb1 100644
--- a/reference/cromwell_jobs.html
+++ b/reference/cromwell_jobs.html
@@ -106,7 +106,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Amy Paguirigan.</p>
+  <p></p><p>Developed by Amy Paguirigan, Scott Chamberlain.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/cromwell_logs.html b/reference/cromwell_logs.html
index feed587..dc9517b 100644
--- a/reference/cromwell_logs.html
+++ b/reference/cromwell_logs.html
@@ -85,7 +85,7 @@ <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a><
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Amy Paguirigan.</p>
+  <p></p><p>Developed by Amy Paguirigan, Scott Chamberlain.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/cromwell_outputs.html b/reference/cromwell_outputs.html
index 3e525b3..bcf6700 100644
--- a/reference/cromwell_outputs.html
+++ b/reference/cromwell_outputs.html
@@ -86,7 +86,7 @@ <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a><
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Amy Paguirigan.</p>
+  <p></p><p>Developed by Amy Paguirigan, Scott Chamberlain.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/cromwell_submit_batch.html b/reference/cromwell_submit_batch.html
index 3b2136d..7def8d5 100644
--- a/reference/cromwell_submit_batch.html
+++ b/reference/cromwell_submit_batch.html
@@ -120,7 +120,7 @@ <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a><
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Amy Paguirigan.</p>
+  <p></p><p>Developed by Amy Paguirigan, Scott Chamberlain.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/cromwell_timing.html b/reference/cromwell_timing.html
index cdc38f9..8eecd43 100644
--- a/reference/cromwell_timing.html
+++ b/reference/cromwell_timing.html
@@ -85,7 +85,7 @@ <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a><
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Amy Paguirigan.</p>
+  <p></p><p>Developed by Amy Paguirigan, Scott Chamberlain.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/cromwell_validate.html b/reference/cromwell_validate.html
index fb41cb9..9b4e75c 100644
--- a/reference/cromwell_validate.html
+++ b/reference/cromwell_validate.html
@@ -92,7 +92,7 @@ <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a><
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Amy Paguirigan.</p>
+  <p></p><p>Developed by Amy Paguirigan, Scott Chamberlain.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/cromwell_version.html b/reference/cromwell_version.html
index f2bd409..3cccd09 100644
--- a/reference/cromwell_version.html
+++ b/reference/cromwell_version.html
@@ -79,7 +79,7 @@ <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a><
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Amy Paguirigan.</p>
+  <p></p><p>Developed by Amy Paguirigan, Scott Chamberlain.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/cromwell_workflow.html b/reference/cromwell_workflow.html
index e915592..bc9aa66 100644
--- a/reference/cromwell_workflow.html
+++ b/reference/cromwell_workflow.html
@@ -101,7 +101,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Amy Paguirigan.</p>
+  <p></p><p>Developed by Amy Paguirigan, Scott Chamberlain.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/index.html b/reference/index.html
index c8ad00d..a9ee94a 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -152,7 +152,7 @@ <h2 id="all-functions">All functions<a class="anchor" aria-label="anchor" href="
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Amy Paguirigan.</p>
+  <p></p><p>Developed by Amy Paguirigan, Scott Chamberlain.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/rcromwell-package.html b/reference/rcromwell-package.html
index ca6ede4..d48765e 100644
--- a/reference/rcromwell-package.html
+++ b/reference/rcromwell-package.html
@@ -61,15 +61,16 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
     </div>
     <div class="section level2">
     <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2>
-    <p><strong>Maintainer</strong>: Amy Paguirigan <a href="mailto:apaguiri@fredhutch.org">apaguiri@fredhutch.org</a> (<a href="https://orcid.org/0000-0002-6819-9736" class="external-link">ORCID</a>)</p>
-    </div>
+    <p><strong>Maintainer</strong>: Scott Chamberlain <a href="mailto:sachamber@fredhutch.org">sachamber@fredhutch.org</a> (<a href="https://orcid.org/0000-0003-1444-9135" class="external-link">ORCID</a>)</p>
+<p>Authors:</p><ul><li><p>Amy Paguirigan (<a href="https://orcid.org/0000-0002-6819-9736" class="external-link">ORCID</a>)</p></li>
+</ul></div>
 
   </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
     </nav></aside></div>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Amy Paguirigan.</p>
+  <p></p><p>Developed by Amy Paguirigan, Scott Chamberlain.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/workflow_inputs.html b/reference/workflow_inputs.html
index c2735df..f77368f 100644
--- a/reference/workflow_inputs.html
+++ b/reference/workflow_inputs.html
@@ -85,7 +85,7 @@ <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a><
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Amy Paguirigan.</p>
+  <p></p><p>Developed by Amy Paguirigan, Scott Chamberlain.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/workflow_options.html b/reference/workflow_options.html
index 513ce93..ed0fd14 100644
--- a/reference/workflow_options.html
+++ b/reference/workflow_options.html
@@ -93,7 +93,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Amy Paguirigan.</p>
+  <p></p><p>Developed by Amy Paguirigan, Scott Chamberlain.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/search.json b/search.json
index 03a2362..2ad6ca5 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":"http://getwilds.org/rcromwell/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2024 rcromwell authors Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"http://getwilds.org/rcromwell/articles/rcromwell.html","id":"set-your-cromwell-url","dir":"Articles","previous_headings":"","what":"Set your Cromwell URL","title":"Getting Started","text":"","code":"cromwell_config(\"http://localhost:8000\") #> $rcromwell_settings #> $rcromwell_settings$url #> [1] \"http://localhost:8000\" #>  #> $rcromwell_settings$verbose #> [1] TRUE"},{"path":"http://getwilds.org/rcromwell/articles/rcromwell.html","id":"send-a-workflow-to-crowmell","dir":"Articles","previous_headings":"","what":"Send a workflow to Crowmell","title":"Getting Started","text":"thisJob$id (af1c9bf4-45ac-4f41-b563-fc7f53676db8) unique Cromwell ID entire workflow - can use request sorts metadata!!!","code":"file_hello <- system.file(\"examples/hello.wdl\", package = \"rcromwell\") file_inputs <- system.file(\"examples/inputs.json\", package = \"rcromwell\") thisJob <- cromwell_submit_batch(wdl = file_hello, params = file_inputs) #> Submitting a batch workflow to Cromwell thisOne <- thisJob$id"},{"path":"http://getwilds.org/rcromwell/articles/rcromwell.html","id":"now-get-all-your-metadata-and-track-the-workflow","dir":"Articles","previous_headings":"","what":"Now get all your metadata and track the workflow!!","title":"Getting Started","text":"Return data frame jobs run past number days (uses database) Return data frame (one line submit one workflow id) containing workflow level metadata Print current status workflow(s) () Return data frame containing call level metadata Handy set dplyr commands tell various calls Returns data frame containing call level call caching metadata","code":"cromwell_jobs(days = 2) #> Querying cromwell for jobs in the last 2 days. #> # A tibble: 52 × 8 #>    workflow_id metadataArchiveStatus workflow_name start status submission end   #>    <chr>       <chr>                 <chr>         <chr> <chr>  <chr>      <chr> #>  1 8c418d8c-c… Unarchived            test          2024… Runni… 2024-01-0… <NA>  #>  2 53ac66b1-a… Unarchived            test          2024… Succe… 2024-01-0… 2024… #>  3 f6f919f5-4… Unarchived            test          2024… Succe… 2024-01-0… 2024… #>  4 f7464c7e-9… Unarchived            test          2024… Succe… 2024-01-0… 2024… #>  5 0a286772-2… Unarchived            test          2024… Succe… 2024-01-0… 2024… #>  6 b0be7e6e-6… Unarchived            test          2024… Succe… 2024-01-0… 2024… #>  7 700c3598-9… Unarchived            test          2024… Succe… 2024-01-0… 2024… #>  8 04bbe5ab-b… Unarchived            test          2024… Succe… 2024-01-0… 2024… #>  9 612b4a6c-4… Unarchived            test          2024… Succe… 2024-01-0… 2024… #> 10 088fb55e-2… Unarchived            test          2024… Succe… 2024-01-0… 2024… #> # ℹ 42 more rows #> # ℹ 1 more variable: workflowDuration <chr> w <- cromwell_workflow(thisOne) #> Querying for metadata for workflow id: af1c9bf4-45ac-4f41-b563-fc7f53676db8 w$status #> [1] \"Running\" df <- cromwell_call(thisOne) #> Querying for call metadata for workflow id: af1c9bf4-45ac-4f41-b563-fc7f53676db8 df %>%   group_by(callName, executionStatus) %>%   summarize(status = n()) %>%   arrange(executionStatus) #> `summarise()` has grouped output by 'callName'. You can override using the #> `.groups` argument. #> # A tibble: 1 × 3 #> # Groups:   callName [1] #>   callName executionStatus status #>   <chr>    <chr>            <int> #> 1 hello    Running              1 cromwell_cache(thisOne) #> Querying for call caching metadata for workflow id: af1c9bf4-45ac-4f41-b563-fc7f53676db8 #> # A tibble: 1 × 8 #>   workflowName callName callCaching.allowResultReuse callCaching.effectiveCall…¹ #>   <chr>        <chr>    <chr>                        <chr>                       #> 1 test         hello    FALSE                        CallCachingOff              #> # ℹ abbreviated name: ¹​callCaching.effectiveCallCachingMode #> # ℹ 4 more variables: inputs.name <chr>, shardIndex <chr>, workflow_id <chr>, #> #   executionStatus <chr>"},{"path":"http://getwilds.org/rcromwell/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Amy Paguirigan. Author, maintainer.","code":""},{"path":"http://getwilds.org/rcromwell/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Paguirigan (2024). rcromwell: Convenience Tools Managing WDL Workflows via Cromwell. R package version 3.0.0http://getwilds.org/rcromwell/ (website) https://github.com/getwilds/rcromwell (devel), http://getwilds.org/rcromwell/ (website)https://github.com/getwilds/rcromwell (devel).","code":"@Manual{,   title = {rcromwell: Convenience Tools for Managing WDL Workflows via Cromwell},   author = {Amy Paguirigan},   year = {2024},   note = {R package version 3.0.0http://getwilds.org/rcromwell/ (website) https://github.com/getwilds/rcromwell (devel)},   url = {http://getwilds.org/rcromwell/ (website) https://github.com/getwilds/rcromwell (devel)}, }"},{"path":"http://getwilds.org/rcromwell/index.html","id":"rcromwell","dir":"","previous_headings":"","what":"Convenience Tools for Managing WDL Workflows via Cromwell","title":"Convenience Tools for Managing WDL Workflows via Cromwell","text":"Convenience Tools Managing WDL Workflows via Cromwell","code":""},{"path":"http://getwilds.org/rcromwell/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Convenience Tools for Managing WDL Workflows via Cromwell","text":"can install development version rcromwell GitHub : Install specific release version (case v1.0) :","code":"# install.packages(\"pak\") pak::pak(\"getwilds/rcromwell\") pak::pak('getwilds/rcromwell@v1.0')"},{"path":"http://getwilds.org/rcromwell/index.html","id":"example-workflow-process","dir":"","previous_headings":"","what":"Example workflow process","title":"Convenience Tools for Managing WDL Workflows via Cromwell","text":"Set Cromwell URL","code":"library(rcromwell) library(dplyr) cromwell_config(\"http://localhost:20202\")"},{"path":"http://getwilds.org/rcromwell/index.html","id":"validate-your-workflow-formatting","dir":"","previous_headings":"Example workflow process","what":"Validate your workflow formatting","title":"Convenience Tools for Managing WDL Workflows via Cromwell","text":"","code":"list.files(pattern = \"*.wdl\") valid <- cromwell_validate(wdl = \"myworkflow.wdl\") valid[[\"errors\"]]"},{"path":"http://getwilds.org/rcromwell/index.html","id":"go-fix-your-issues-now-send-your-workflow-to-crowmell","dir":"","previous_headings":"Example workflow process","what":"Go fix your issues, now send your workflow to Crowmell","title":"Convenience Tools for Managing WDL Workflows via Cromwell","text":"thisJob$id unique Cromwell ID entire workflow - can use request sorts metadata!!!","code":"thisJob <- cromwell_submit_batch(wdl = \"myworkflow.wdl\",                     params = \"myworkflow-parameters.json\",                     batch = \"myworkflow-batch.json\",                     options = \"workflow-options.json\") (thisOne <- thisJob$id)"},{"path":"http://getwilds.org/rcromwell/index.html","id":"now-get-all-your-metadata-and-track-the-workflow","dir":"","previous_headings":"Example workflow process","what":"Now get all your metadata and track the workflow!!","title":"Convenience Tools for Managing WDL Workflows via Cromwell","text":"Return data frame jobs run past number days (uses database) Return data frame (one line submit one workflow id) containing workflow level metadata Print current status workflow(s) () Return data frame containing call level metadata Handy set dplyr commands tell various calls Returns data frame containing call level call caching metadata Handy set dplyr commands tell sort call caching happening Opens popup browser timing diagram . Returns data frame containing call level failure metadata tell Cromwell abort current workflow - note undone take stop jobs. workflow done, request information workflow outputs.","code":"cromwell_jobs(days = 2) w <- cromwell_workflow(thisOne) w$status df <- cromwell_call(thisOne) df %>%   group_by(callName, executionStatus) %>%   summarize(status = n()) %>%   arrange(executionStatus) ca <- cromwell_cache(thisOne) ca %>%   group_by(callCaching.hit, callName) %>%   summarize(hits = n()) cromwell_timing(thisOne) cromwell_failures(thisOne) cromwell_abort(thisOne) cromwell_outputs(thisOne)"},{"path":"http://getwilds.org/rcromwell/index.html","id":"misc-stuff","dir":"","previous_headings":"Example workflow process","what":"Misc stuff","title":"Convenience Tools for Managing WDL Workflows via Cromwell","text":"Ugly list raw metadata need workflow troubleshooting","code":"wtf <- cromwell_glob(thisOne) wtf[[\"failures\"]]"},{"path":"http://getwilds.org/rcromwell/reference/cromwellSettings.html","id":null,"dir":"Reference","previous_headings":"","what":"Cromwell Settings — cromwellSettings","title":"Cromwell Settings — cromwellSettings","text":"Cromwell Settings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwellSettings.html","id":"cromwell-url","dir":"Reference","previous_headings":"","what":"Cromwell URL","title":"Cromwell Settings — cromwellSettings","text":"URL Cromwell server interacting required. way setting env var: CROMWELLURL can set env var many different ways. within R can cromwell_config() like: cromwell_config(url = \"/url\") equivalent Sys.setenv(CROMWELLURL = \"/url\") Note sets url current R session persist among R sessions. options include: Set CROMWELLURL env var .bash_profile file equivalent picked R starts. Set CROMWELLURL env var IDE RStudio. Set CROMWELLURL env var prefixing R command line, e.g., CROMWELLURL=http:///url R","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwellSettings.html","id":"verbose-messaging","dir":"Reference","previous_headings":"","what":"Verbose messaging","title":"Cromwell Settings — cromwellSettings","text":"can set preference whether get messages informing various tasks rcromwell performing. See cromwell_config()","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_abort.html","id":null,"dir":"Reference","previous_headings":"","what":"Abort a workflow job on Cromwell — cromwell_abort","title":"Abort a workflow job on Cromwell — cromwell_abort","text":"Abort workflow job Cromwell","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_abort.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Abort a workflow job on Cromwell — cromwell_abort","text":"","code":"cromwell_abort(workflow_id)"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_abort.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Abort a workflow job on Cromwell — cromwell_abort","text":"workflow_id (character) single workflow ID","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_abort.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Abort a workflow job on Cromwell — cromwell_abort","text":"Returns response API post","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_abort.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Abort a workflow job on Cromwell — cromwell_abort","text":"Requires valid Cromwell server URL set. See cromwellSettings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_abort.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Abort a workflow job on Cromwell — cromwell_abort","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_backends.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the available backends of a Cromwell server — cromwell_backends","title":"Get the available backends of a Cromwell server — cromwell_backends","text":"Get available backends Cromwell server","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_backends.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the available backends of a Cromwell server — cromwell_backends","text":"","code":"cromwell_backends()"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_backends.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get the available backends of a Cromwell server — cromwell_backends","text":"Cromwell backend options","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_backends.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Get the available backends of a Cromwell server — cromwell_backends","text":"Requires valid Cromwell server URL set. See cromwellSettings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_backends.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Get the available backends of a Cromwell server — cromwell_backends","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_cache.html","id":null,"dir":"Reference","previous_headings":"","what":"Pull Cromwell Call Caching Data — cromwell_cache","title":"Pull Cromwell Call Caching Data — cromwell_cache","text":"Gets info call caching status calls workflow","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_cache.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pull Cromwell Call Caching Data — cromwell_cache","text":"","code":"cromwell_cache(workflow_id)"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_cache.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pull Cromwell Call Caching Data — cromwell_cache","text":"workflow_id (character) single workflow ID","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_cache.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pull Cromwell Call Caching Data — cromwell_cache","text":"Returns long form data frame metadata call caching workflow. NOTE: Currently support subworkflows well.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_cache.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Pull Cromwell Call Caching Data — cromwell_cache","text":"Requires valid Cromwell server URL set. See cromwellSettings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_cache.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Pull Cromwell Call Caching Data — cromwell_cache","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_call.html","id":null,"dir":"Reference","previous_headings":"","what":"Retrieve metadata for the calls made in a Cromwell workflow job — cromwell_call","title":"Retrieve metadata for the calls made in a Cromwell workflow job — cromwell_call","text":"Retrieve process call metadata specific workflow.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_call.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retrieve metadata for the calls made in a Cromwell workflow job — cromwell_call","text":"","code":"cromwell_call(workflow_id)"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_call.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Retrieve metadata for the calls made in a Cromwell workflow job — cromwell_call","text":"workflow_id (character) single workflow ID","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_call.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Retrieve metadata for the calls made in a Cromwell workflow job — cromwell_call","text":"Returns long form data frame metadata calls. NOTE: currently support subWorkflows well yet.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_call.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Retrieve metadata for the calls made in a Cromwell workflow job — cromwell_call","text":"Now supports nested scatters.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_call.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Retrieve metadata for the calls made in a Cromwell workflow job — cromwell_call","text":"Requires valid Cromwell server URL set. See cromwellSettings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_call.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Retrieve metadata for the calls made in a Cromwell workflow job — cromwell_call","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_call.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Retrieve metadata for the calls made in a Cromwell workflow job — cromwell_call","text":"","code":"if (FALSE) { ## Request what jobs have been submitted to your Cromwell instance in the ## past 7 days. recentJobs <- cromwell_jobs(days = 7) ## Request workflow metadata for a specific job that was run in your ## Cromwell instance. thisWorkflowID <- recentJobs$workflow_id[1] callsMeta <- cromwell_call(workflow_id = thisWorkflowID) }"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_config.html","id":null,"dir":"Reference","previous_headings":"","what":"Cromwell Configuration — cromwell_config","title":"Cromwell Configuration — cromwell_config","text":"Cromwell Configuration","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_config.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cromwell Configuration — cromwell_config","text":"","code":"cromwell_config(cromwell_url = NULL, verbose = TRUE)"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_config.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cromwell Configuration — cromwell_config","text":"cromwell_url (character) Cromwell server URL. full url, example \"http://localhost:8000\" \"https://mycromwell.com\" verbose (logical) verbose messaging. default: TRUE. toggles (TRUE) (FALSE) messages throughout package.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_config.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Cromwell Configuration — cromwell_config","text":"Note although default value cromwell_url NULL, fetch current value CROMWELLURL env var internally cromwell_url=NULL - thus, retain value CROMWELLURL set even function run without passing anything cromwell_url","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_config.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Cromwell Configuration — cromwell_config","text":"Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_config.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Cromwell Configuration — cromwell_config","text":"","code":"if (FALSE) { cromwell_config() cromwell_config(\"https://mycromwellinstance.com\") cromwell_config(verbose = FALSE) }"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_failures.html","id":null,"dir":"Reference","previous_headings":"","what":"Pull metadata for the failed calls made in a Cromwell workflow job — cromwell_failures","title":"Pull metadata for the failed calls made in a Cromwell workflow job — cromwell_failures","text":"Gets info failed calls specific workflow","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_failures.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pull metadata for the failed calls made in a Cromwell workflow job — cromwell_failures","text":"","code":"cromwell_failures(workflow_id)"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_failures.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pull metadata for the failed calls made in a Cromwell workflow job — cromwell_failures","text":"workflow_id (character) single workflow ID","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_failures.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pull metadata for the failed calls made in a Cromwell workflow job — cromwell_failures","text":"Returns long form data frame metadata failed calls workflow.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_failures.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Pull metadata for the failed calls made in a Cromwell workflow job — cromwell_failures","text":"Requires valid Cromwell server URL set. See cromwellSettings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_failures.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Pull metadata for the failed calls made in a Cromwell workflow job — cromwell_failures","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_failures.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Pull metadata for the failed calls made in a Cromwell workflow job — cromwell_failures","text":"","code":"if (FALSE) { ## Request what jobs have been submitted to your Cromwell instance in the ## past 7 days. recentJobs <- cromwell_jobs(days = 7) ## Request workflow metadata for a specific job that was run in your ## Cromwell instance. thisWorkflowID <- recentJobs$workflow_id[1] failsMeta <- cromwell_failures(workflow_id = thisWorkflowID) }"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_glob.html","id":null,"dir":"Reference","previous_headings":"","what":"Pull a glob of metadata for a specific Cromwell workflow job — cromwell_glob","title":"Pull a glob of metadata for a specific Cromwell workflow job — cromwell_glob","text":"Retrieve glob workflow level metadata specific workflow.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_glob.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pull a glob of metadata for a specific Cromwell workflow job — cromwell_glob","text":"","code":"cromwell_glob(workflow_id, expand_sub_workflows = FALSE)"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_glob.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pull a glob of metadata for a specific Cromwell workflow job — cromwell_glob","text":"workflow_id (character) single workflow ID expand_sub_workflows Boolean, whether expand subworkflows results , default FALSE.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_glob.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pull a glob of metadata for a specific Cromwell workflow job — cromwell_glob","text":"Returns gross list lists metadata workflow.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_glob.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Pull a glob of metadata for a specific Cromwell workflow job — cromwell_glob","text":"Requires valid Cromwell server URL set. See cromwellSettings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_glob.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Pull a glob of metadata for a specific Cromwell workflow job — cromwell_glob","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_glob.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Pull a glob of metadata for a specific Cromwell workflow job — cromwell_glob","text":"","code":"if (FALSE) { ## Request what jobs have been submitted to your Cromwell instance in the ## past 7 days. recentJobs <- cromwell_jobs(days = 7) ## Request workflow metadata for a specific job that was run in your ## Cromwell instance. thisWorkflowID <- recentJobs$workflow_id[1] workflowMeta <- cromwell_glob(workflow_id = thisWorkflowID) }"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_jobs.html","id":null,"dir":"Reference","previous_headings":"","what":"Requests metadata about Cromwell workflow jobs during a time period specified — cromwell_jobs","title":"Requests metadata about Cromwell workflow jobs during a time period specified — cromwell_jobs","text":"Requests metadata Cromwell workflow jobs time period specified","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_jobs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Requests metadata about Cromwell workflow jobs during a time period specified — cromwell_jobs","text":"","code":"cromwell_jobs(days = 1, workflow_name = NULL, workflow_status = NULL)"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_jobs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Requests metadata about Cromwell workflow jobs during a time period specified — cromwell_jobs","text":"days number days history return, defaults 1 day. workflow_name array strings valid workflow names want job list. workflow_status array strings valid workflow statuses want job list (e.g., submitted, running, succeeded, failed, aborting, aborted)","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_jobs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Requests metadata about Cromwell workflow jobs during a time period specified — cromwell_jobs","text":"Returns long form data frame metadata workflow jobs submitted specific Cromwell instance.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_jobs.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Requests metadata about Cromwell workflow jobs during a time period specified — cromwell_jobs","text":"Requires valid Cromwell server URL set. See cromwellSettings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_jobs.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Requests metadata about Cromwell workflow jobs during a time period specified — cromwell_jobs","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_jobs.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Requests metadata about Cromwell workflow jobs during a time period specified — cromwell_jobs","text":"","code":"if (FALSE) { ## Request what jobs have been submitted to your Cromwell instance in the ## past 7 days. recentJobs <- cromwell_jobs(days = 7) }"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_logs.html","id":null,"dir":"Reference","previous_headings":"","what":"Gets logs for a workflow in Cromwell — cromwell_logs","title":"Gets logs for a workflow in Cromwell — cromwell_logs","text":"Gets logs workflow Cromwell","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_logs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Gets logs for a workflow in Cromwell — cromwell_logs","text":"","code":"cromwell_logs(workflow_id)"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_logs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Gets logs for a workflow in Cromwell — cromwell_logs","text":"workflow_id (character) single workflow ID","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_logs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Gets logs for a workflow in Cromwell — cromwell_logs","text":"Returns response API post","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_logs.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Gets logs for a workflow in Cromwell — cromwell_logs","text":"Requires valid Cromwell server URL set. See cromwellSettings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_logs.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Gets logs for a workflow in Cromwell — cromwell_logs","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_outputs.html","id":null,"dir":"Reference","previous_headings":"","what":"Gets outputs for a workflow in Cromwell — cromwell_outputs","title":"Gets outputs for a workflow in Cromwell — cromwell_outputs","text":"Gets outputs workflow Cromwell","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_outputs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Gets outputs for a workflow in Cromwell — cromwell_outputs","text":"","code":"cromwell_outputs(workflow_id)"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_outputs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Gets outputs for a workflow in Cromwell — cromwell_outputs","text":"workflow_id (character) single workflow ID","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_outputs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Gets outputs for a workflow in Cromwell — cromwell_outputs","text":"Returns dataframe containing workflowName, workflowOutputType, pathToOutput, shardIndex specified outputs workflow_id","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_outputs.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Gets outputs for a workflow in Cromwell — cromwell_outputs","text":"Requires valid Cromwell server URL set. See cromwellSettings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_outputs.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Gets outputs for a workflow in Cromwell — cromwell_outputs","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_submit_batch.html","id":null,"dir":"Reference","previous_headings":"","what":"Submit a workflow job to Cromwell — cromwell_submit_batch","title":"Submit a workflow job to Cromwell — cromwell_submit_batch","text":"Supports submission fully defined workflow job Cromwell instance.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_submit_batch.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Submit a workflow job to Cromwell — cromwell_submit_batch","text":"","code":"cromwell_submit_batch(   wdl,   batch = NULL,   params = NULL,   options = NULL,   labels = NULL,   dependencies = NULL )"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_submit_batch.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Submit a workflow job to Cromwell — cromwell_submit_batch","text":"wdl Local path wdl file describing workflow. (Required) batch Local path json containing reference batch file desired workflow batch. (Optional) params Local path json containing parameters use workflow. (Optional) options Local path json containing workflow options apply. (Optional) labels data frame containing labels workflow. (Optional) dependencies zip'd file subworkflow dependencies. (Optional)","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_submit_batch.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Submit a workflow job to Cromwell — cromwell_submit_batch","text":"Returns response API post includes workflow ID need monitor job.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_submit_batch.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Submit a workflow job to Cromwell — cromwell_submit_batch","text":"Requires valid Cromwell server URL set. See cromwellSettings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_submit_batch.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Submit a workflow job to Cromwell — cromwell_submit_batch","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_timing.html","id":null,"dir":"Reference","previous_headings":"","what":"Get a timing diagram for a Cromwell workflow — cromwell_timing","title":"Get a timing diagram for a Cromwell workflow — cromwell_timing","text":"Get timing diagram Cromwell workflow","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_timing.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get a timing diagram for a Cromwell workflow — cromwell_timing","text":"","code":"cromwell_timing(workflow_id)"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_timing.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get a timing diagram for a Cromwell workflow — cromwell_timing","text":"workflow_id (character) single workflow ID","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_timing.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get a timing diagram for a Cromwell workflow — cromwell_timing","text":"Opens timing diagram browser","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_timing.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Get a timing diagram for a Cromwell workflow — cromwell_timing","text":"Requires valid Cromwell server URL set. See cromwellSettings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_timing.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Get a timing diagram for a Cromwell workflow — cromwell_timing","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_validate.html","id":null,"dir":"Reference","previous_headings":"","what":"Validates a workflow for submission — cromwell_validate","title":"Validates a workflow for submission — cromwell_validate","text":"Validates workflow submission","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_validate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Validates a workflow for submission — cromwell_validate","text":"","code":"cromwell_validate(wdl, all_inputs = NULL)"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_validate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Validates a workflow for submission — cromwell_validate","text":"wdl Local path wdl file describing workflow. (Required) all_inputs Local path json containing inputs parameters use workflow - batch parameters json present must first combined. (Optional)","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_validate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Validates a workflow for submission — cromwell_validate","text":"Returns response API post includes workflow ID need monitor job.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_validate.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Validates a workflow for submission — cromwell_validate","text":"Requires valid Cromwell server URL set. See cromwellSettings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_validate.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Validates a workflow for submission — cromwell_validate","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_version.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the version of a Cromwell server — cromwell_version","title":"Get the version of a Cromwell server — cromwell_version","text":"Get version Cromwell server","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_version.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the version of a Cromwell server — cromwell_version","text":"","code":"cromwell_version()"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_version.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get the version of a Cromwell server — cromwell_version","text":"(character) Cromwell version","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_version.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Get the version of a Cromwell server — cromwell_version","text":"Requires valid Cromwell server URL set. See cromwellSettings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_version.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Get the version of a Cromwell server — cromwell_version","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_workflow.html","id":null,"dir":"Reference","previous_headings":"","what":"Pull metadata for a specific Cromwell workflow job — cromwell_workflow","title":"Pull metadata for a specific Cromwell workflow job — cromwell_workflow","text":"Retrieve process labels, submission workflow level metadata specific workflow.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_workflow.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pull metadata for a specific Cromwell workflow job — cromwell_workflow","text":"","code":"cromwell_workflow(workflow_id)"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_workflow.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pull metadata for a specific Cromwell workflow job — cromwell_workflow","text":"workflow_id (character) single workflow ID","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_workflow.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pull metadata for a specific Cromwell workflow job — cromwell_workflow","text":"Returns long form data frame metadata workflow.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_workflow.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Pull metadata for a specific Cromwell workflow job — cromwell_workflow","text":"Requires valid Cromwell server URL set. See cromwellSettings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_workflow.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Pull metadata for a specific Cromwell workflow job — cromwell_workflow","text":"Amy Paguirigan","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_workflow.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Pull metadata for a specific Cromwell workflow job — cromwell_workflow","text":"","code":"if (FALSE) { ## Request what jobs have been submitted to your Cromwell instance in the ## past 7 days. recentJobs <- cromwell_jobs(days = 7) ## Request workflow metadata for a specific job that was run in your ## Cromwell instance. thisWorkflowID <- recentJobs$workflow_id[1] workflowMeta <- cromwell_workflow(workflow_id = thisWorkflowID) }"},{"path":"http://getwilds.org/rcromwell/reference/rcromwell-package.html","id":null,"dir":"Reference","previous_headings":"","what":"rcromwell: Convenience Tools for Managing WDL Workflows via Cromwell — rcromwell-package","title":"rcromwell: Convenience Tools for Managing WDL Workflows via Cromwell — rcromwell-package","text":"repo containing basic R package using Cromwell WDL workflows via R.","code":""},{"path":[]},{"path":"http://getwilds.org/rcromwell/reference/rcromwell-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"rcromwell: Convenience Tools for Managing WDL Workflows via Cromwell — rcromwell-package","text":"Maintainer: Amy Paguirigan apaguiri@fredhutch.org (ORCID)","code":""},{"path":"http://getwilds.org/rcromwell/reference/workflow_inputs.html","id":null,"dir":"Reference","previous_headings":"","what":"Pull the workflow inputs provided for a Cromwell workflow job — workflow_inputs","title":"Pull the workflow inputs provided for a Cromwell workflow job — workflow_inputs","text":"Pull workflow inputs provided Cromwell workflow job","code":""},{"path":"http://getwilds.org/rcromwell/reference/workflow_inputs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pull the workflow inputs provided for a Cromwell workflow job — workflow_inputs","text":"","code":"workflow_inputs(workflow_id)"},{"path":"http://getwilds.org/rcromwell/reference/workflow_inputs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pull the workflow inputs provided for a Cromwell workflow job — workflow_inputs","text":"workflow_id (character) single workflow ID","code":""},{"path":"http://getwilds.org/rcromwell/reference/workflow_inputs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pull the workflow inputs provided for a Cromwell workflow job — workflow_inputs","text":"Returns data frame inputs workflow previously run","code":""},{"path":"http://getwilds.org/rcromwell/reference/workflow_inputs.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Pull the workflow inputs provided for a Cromwell workflow job — workflow_inputs","text":"Requires valid Cromwell server URL set. See cromwellSettings","code":""},{"path":"http://getwilds.org/rcromwell/reference/workflow_inputs.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Pull the workflow inputs provided for a Cromwell workflow job — workflow_inputs","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/workflow_options.html","id":null,"dir":"Reference","previous_headings":"","what":"Pull the workflow options provided for a Cromwell workflow job — workflow_options","title":"Pull the workflow options provided for a Cromwell workflow job — workflow_options","text":"Pull workflow options provided Cromwell workflow job","code":""},{"path":"http://getwilds.org/rcromwell/reference/workflow_options.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pull the workflow options provided for a Cromwell workflow job — workflow_options","text":"","code":"workflow_options(workflow_id)"},{"path":"http://getwilds.org/rcromwell/reference/workflow_options.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pull the workflow options provided for a Cromwell workflow job — workflow_options","text":"workflow_id (character) single workflow ID","code":""},{"path":"http://getwilds.org/rcromwell/reference/workflow_options.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pull the workflow options provided for a Cromwell workflow job — workflow_options","text":"Returns data frame options workflow previously run","code":""},{"path":"http://getwilds.org/rcromwell/reference/workflow_options.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Pull the workflow options provided for a Cromwell workflow job — workflow_options","text":"Requires valid Cromwell server URL set. See cromwellSettings","code":""},{"path":"http://getwilds.org/rcromwell/reference/workflow_options.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Pull the workflow options provided for a Cromwell workflow job — workflow_options","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/workflow_options.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Pull the workflow options provided for a Cromwell workflow job — workflow_options","text":"","code":"if (FALSE) { jobs <- cromwell_jobs() workflow_options(jobs$workflow_id[1]) }"},{"path":"http://getwilds.org/rcromwell/news/index.html","id":"rcromwell-300","dir":"Changelog","previous_headings":"","what":"rcromwell 3.0.0","title":"rcromwell 3.0.0","text":"First version package new name rcromwell Functions functions arguments changed camelCase snake_case Package now tests Package documentation added http://getwilds.org/rcromwell/","code":""}]
+[{"path":[]},{"path":"http://getwilds.org/rcromwell/CODE_OF_CONDUCT.html","id":"our-pledge","dir":"","previous_headings":"","what":"Our Pledge","title":"Contributor Covenant Code of Conduct","text":"members, contributors, leaders pledge make participation community harassment-free experience everyone, regardless age, body size, visible invisible disability, ethnicity, sex characteristics, gender identity expression, level experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, sexual identity orientation. pledge act interact ways contribute open, welcoming, diverse, inclusive, healthy community.","code":""},{"path":"http://getwilds.org/rcromwell/CODE_OF_CONDUCT.html","id":"our-standards","dir":"","previous_headings":"","what":"Our Standards","title":"Contributor Covenant Code of Conduct","text":"Examples behavior contributes positive environment community include: Demonstrating empathy kindness toward people respectful differing opinions, viewpoints, experiences Giving gracefully accepting constructive feedback Accepting responsibility apologizing affected mistakes, learning experience Focusing best just us individuals, overall community Examples unacceptable behavior include: use sexualized language imagery, sexual attention advances kind Trolling, insulting derogatory comments, personal political attacks Public private harassment Publishing others’ private information, physical email address, without explicit permission conduct reasonably considered inappropriate professional setting","code":""},{"path":"http://getwilds.org/rcromwell/CODE_OF_CONDUCT.html","id":"enforcement-responsibilities","dir":"","previous_headings":"","what":"Enforcement Responsibilities","title":"Contributor Covenant Code of Conduct","text":"Community leaders responsible clarifying enforcing standards acceptable behavior take appropriate fair corrective action response behavior deem inappropriate, threatening, offensive, harmful. Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"http://getwilds.org/rcromwell/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. Examples representing community include using official e-mail address, posting via official social media account, acting appointed representative online offline event.","code":""},{"path":"http://getwilds.org/rcromwell/CODE_OF_CONDUCT.html","id":"enforcement","dir":"","previous_headings":"","what":"Enforcement","title":"Contributor Covenant Code of Conduct","text":"Instances abusive, harassing, otherwise unacceptable behavior may reported community leaders responsible enforcement sachamber@fredhutch.org. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"http://getwilds.org/rcromwell/CODE_OF_CONDUCT.html","id":"enforcement-guidelines","dir":"","previous_headings":"","what":"Enforcement Guidelines","title":"Contributor Covenant Code of Conduct","text":"Community leaders follow Community Impact Guidelines determining consequences action deem violation Code Conduct:","code":""},{"path":"http://getwilds.org/rcromwell/CODE_OF_CONDUCT.html","id":"id_1-correction","dir":"","previous_headings":"Enforcement Guidelines","what":"1. Correction","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Use inappropriate language behavior deemed unprofessional unwelcome community. Consequence: private, written warning community leaders, providing clarity around nature violation explanation behavior inappropriate. public apology may requested.","code":""},{"path":"http://getwilds.org/rcromwell/CODE_OF_CONDUCT.html","id":"id_2-warning","dir":"","previous_headings":"Enforcement Guidelines","what":"2. Warning","title":"Contributor Covenant Code of Conduct","text":"Community Impact: violation single incident series actions. Consequence: warning consequences continued behavior. interaction people involved, including unsolicited interaction enforcing Code Conduct, specified period time. includes avoiding interactions community spaces well external channels like social media. Violating terms may lead temporary permanent ban.","code":""},{"path":"http://getwilds.org/rcromwell/CODE_OF_CONDUCT.html","id":"id_3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"http://getwilds.org/rcromwell/CODE_OF_CONDUCT.html","id":"id_4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"http://getwilds.org/rcromwell/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.1, available https://www.contributor-covenant.org/version/2/1/code_of_conduct.html. Community Impact Guidelines inspired [Mozilla’s code conduct enforcement ladder][https://github.com/mozilla/inclusion]. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https://www.contributor-covenant.org/translations.","code":""},{"path":"http://getwilds.org/rcromwell/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2024 rcromwell authors Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"http://getwilds.org/rcromwell/articles/rcromwell.html","id":"set-your-cromwell-url","dir":"Articles","previous_headings":"","what":"Set your Cromwell URL","title":"Getting Started","text":"","code":"cromwell_config(\"http://localhost:8000\") #> $rcromwell_settings #> $rcromwell_settings$url #> [1] \"http://localhost:8000\" #>  #> $rcromwell_settings$verbose #> [1] TRUE"},{"path":"http://getwilds.org/rcromwell/articles/rcromwell.html","id":"send-a-workflow-to-crowmell","dir":"Articles","previous_headings":"","what":"Send a workflow to Crowmell","title":"Getting Started","text":"thisJob$id (af1c9bf4-45ac-4f41-b563-fc7f53676db8) unique Cromwell ID entire workflow - can use request sorts metadata!!!","code":"file_hello <- system.file(\"examples/hello.wdl\", package = \"rcromwell\") file_inputs <- system.file(\"examples/inputs.json\", package = \"rcromwell\") thisJob <- cromwell_submit_batch(wdl = file_hello, params = file_inputs) #> Submitting a batch workflow to Cromwell thisOne <- thisJob$id"},{"path":"http://getwilds.org/rcromwell/articles/rcromwell.html","id":"now-get-all-your-metadata-and-track-the-workflow","dir":"Articles","previous_headings":"","what":"Now get all your metadata and track the workflow!!","title":"Getting Started","text":"Return data frame jobs run past number days (uses database) Return data frame (one line submit one workflow id) containing workflow level metadata Print current status workflow(s) () Return data frame containing call level metadata Handy set dplyr commands tell various calls Returns data frame containing call level call caching metadata","code":"cromwell_jobs(days = 2) #> Querying cromwell for jobs in the last 2 days. #> # A tibble: 52 × 8 #>    workflow_id metadataArchiveStatus workflow_name start status submission end   #>    <chr>       <chr>                 <chr>         <chr> <chr>  <chr>      <chr> #>  1 8c418d8c-c… Unarchived            test          2024… Runni… 2024-01-0… <NA>  #>  2 53ac66b1-a… Unarchived            test          2024… Succe… 2024-01-0… 2024… #>  3 f6f919f5-4… Unarchived            test          2024… Succe… 2024-01-0… 2024… #>  4 f7464c7e-9… Unarchived            test          2024… Succe… 2024-01-0… 2024… #>  5 0a286772-2… Unarchived            test          2024… Succe… 2024-01-0… 2024… #>  6 b0be7e6e-6… Unarchived            test          2024… Succe… 2024-01-0… 2024… #>  7 700c3598-9… Unarchived            test          2024… Succe… 2024-01-0… 2024… #>  8 04bbe5ab-b… Unarchived            test          2024… Succe… 2024-01-0… 2024… #>  9 612b4a6c-4… Unarchived            test          2024… Succe… 2024-01-0… 2024… #> 10 088fb55e-2… Unarchived            test          2024… Succe… 2024-01-0… 2024… #> # ℹ 42 more rows #> # ℹ 1 more variable: workflowDuration <chr> w <- cromwell_workflow(thisOne) #> Querying for metadata for workflow id: af1c9bf4-45ac-4f41-b563-fc7f53676db8 w$status #> [1] \"Running\" df <- cromwell_call(thisOne) #> Querying for call metadata for workflow id: af1c9bf4-45ac-4f41-b563-fc7f53676db8 df %>%   group_by(callName, executionStatus) %>%   summarize(status = n()) %>%   arrange(executionStatus) #> `summarise()` has grouped output by 'callName'. You can override using the #> `.groups` argument. #> # A tibble: 1 × 3 #> # Groups:   callName [1] #>   callName executionStatus status #>   <chr>    <chr>            <int> #> 1 hello    Running              1 cromwell_cache(thisOne) #> Querying for call caching metadata for workflow id: af1c9bf4-45ac-4f41-b563-fc7f53676db8 #> # A tibble: 1 × 8 #>   workflowName callName callCaching.allowResultReuse callCaching.effectiveCall…¹ #>   <chr>        <chr>    <chr>                        <chr>                       #> 1 test         hello    FALSE                        CallCachingOff              #> # ℹ abbreviated name: ¹​callCaching.effectiveCallCachingMode #> # ℹ 4 more variables: inputs.name <chr>, shardIndex <chr>, workflow_id <chr>, #> #   executionStatus <chr>"},{"path":"http://getwilds.org/rcromwell/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Amy Paguirigan. Author. Scott Chamberlain. Author, maintainer.","code":""},{"path":"http://getwilds.org/rcromwell/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Paguirigan , Chamberlain S (2024). rcromwell: Convenience Tools Managing WDL Workflows via Cromwell. R package version 3.0.0http://getwilds.org/rcromwell/ (website) https://github.com/getwilds/rcromwell (devel), http://getwilds.org/rcromwell/ (website)https://github.com/getwilds/rcromwell (devel).","code":"@Manual{,   title = {rcromwell: Convenience Tools for Managing WDL Workflows via Cromwell},   author = {Amy Paguirigan and Scott Chamberlain},   year = {2024},   note = {R package version 3.0.0http://getwilds.org/rcromwell/ (website) https://github.com/getwilds/rcromwell (devel)},   url = {http://getwilds.org/rcromwell/ (website) https://github.com/getwilds/rcromwell (devel)}, }"},{"path":"http://getwilds.org/rcromwell/index.html","id":"rcromwell","dir":"","previous_headings":"","what":"Convenience Tools for Managing WDL Workflows via Cromwell","title":"Convenience Tools for Managing WDL Workflows via Cromwell","text":"Convenience Tools Managing WDL Workflows via Cromwell Cromwell scientific workflow engine designed simplicity scalability. ’s maintained Broad Institute. (docs, code source). rcromwell maintained Fred Hutch Cancer Center Data Science Lab.","code":""},{"path":"http://getwilds.org/rcromwell/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Convenience Tools for Managing WDL Workflows via Cromwell","text":"can install development version rcromwell GitHub : Install specific release version (case v1.0) :","code":"# install.packages(\"pak\") pak::pak(\"getwilds/rcromwell\") pak::pak('getwilds/rcromwell@v1.1.0')"},{"path":"http://getwilds.org/rcromwell/index.html","id":"documentation","dir":"","previous_headings":"","what":"Documentation","title":"Convenience Tools for Managing WDL Workflows via Cromwell","text":"Go http://getwilds.org/rcromwell/ rcromwell package documentation. Go Get Started vignette get started!","code":""},{"path":"http://getwilds.org/rcromwell/index.html","id":"bugs-features","dir":"","previous_headings":"","what":"Bugs? Features?","title":"Convenience Tools for Managing WDL Workflows via Cromwell","text":"Open issue issue tracker.","code":""},{"path":"http://getwilds.org/rcromwell/index.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"Convenience Tools for Managing WDL Workflows via Cromwell","text":"Please note rcromwell project released Contributor Code Conduct. contributing project, agree abide terms.","code":""},{"path":"http://getwilds.org/rcromwell/index.html","id":"license","dir":"","previous_headings":"","what":"License","title":"Convenience Tools for Managing WDL Workflows via Cromwell","text":"MIT","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwellSettings.html","id":null,"dir":"Reference","previous_headings":"","what":"Cromwell Settings — cromwellSettings","title":"Cromwell Settings — cromwellSettings","text":"Cromwell Settings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwellSettings.html","id":"cromwell-url","dir":"Reference","previous_headings":"","what":"Cromwell URL","title":"Cromwell Settings — cromwellSettings","text":"URL Cromwell server interacting required. way setting env var: CROMWELLURL can set env var many different ways. within R can cromwell_config() like: cromwell_config(url = \"/url\") equivalent Sys.setenv(CROMWELLURL = \"/url\") Note sets url current R session persist among R sessions. options include: Set CROMWELLURL env var .bash_profile file equivalent picked R starts. Set CROMWELLURL env var IDE RStudio. Set CROMWELLURL env var prefixing R command line, e.g., CROMWELLURL=http:///url R","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwellSettings.html","id":"verbose-messaging","dir":"Reference","previous_headings":"","what":"Verbose messaging","title":"Cromwell Settings — cromwellSettings","text":"can set preference whether get messages informing various tasks rcromwell performing. See cromwell_config()","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_abort.html","id":null,"dir":"Reference","previous_headings":"","what":"Abort a workflow job on Cromwell — cromwell_abort","title":"Abort a workflow job on Cromwell — cromwell_abort","text":"Abort workflow job Cromwell","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_abort.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Abort a workflow job on Cromwell — cromwell_abort","text":"","code":"cromwell_abort(workflow_id)"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_abort.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Abort a workflow job on Cromwell — cromwell_abort","text":"workflow_id (character) single workflow ID","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_abort.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Abort a workflow job on Cromwell — cromwell_abort","text":"Returns response API post","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_abort.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Abort a workflow job on Cromwell — cromwell_abort","text":"Requires valid Cromwell server URL set. See cromwellSettings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_abort.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Abort a workflow job on Cromwell — cromwell_abort","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_backends.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the available backends of a Cromwell server — cromwell_backends","title":"Get the available backends of a Cromwell server — cromwell_backends","text":"Get available backends Cromwell server","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_backends.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the available backends of a Cromwell server — cromwell_backends","text":"","code":"cromwell_backends()"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_backends.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get the available backends of a Cromwell server — cromwell_backends","text":"Cromwell backend options","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_backends.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Get the available backends of a Cromwell server — cromwell_backends","text":"Requires valid Cromwell server URL set. See cromwellSettings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_backends.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Get the available backends of a Cromwell server — cromwell_backends","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_cache.html","id":null,"dir":"Reference","previous_headings":"","what":"Pull Cromwell Call Caching Data — cromwell_cache","title":"Pull Cromwell Call Caching Data — cromwell_cache","text":"Gets info call caching status calls workflow","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_cache.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pull Cromwell Call Caching Data — cromwell_cache","text":"","code":"cromwell_cache(workflow_id)"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_cache.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pull Cromwell Call Caching Data — cromwell_cache","text":"workflow_id (character) single workflow ID","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_cache.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pull Cromwell Call Caching Data — cromwell_cache","text":"Returns long form data frame metadata call caching workflow. NOTE: Currently support subworkflows well.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_cache.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Pull Cromwell Call Caching Data — cromwell_cache","text":"Requires valid Cromwell server URL set. See cromwellSettings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_cache.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Pull Cromwell Call Caching Data — cromwell_cache","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_call.html","id":null,"dir":"Reference","previous_headings":"","what":"Retrieve metadata for the calls made in a Cromwell workflow job — cromwell_call","title":"Retrieve metadata for the calls made in a Cromwell workflow job — cromwell_call","text":"Retrieve process call metadata specific workflow.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_call.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retrieve metadata for the calls made in a Cromwell workflow job — cromwell_call","text":"","code":"cromwell_call(workflow_id)"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_call.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Retrieve metadata for the calls made in a Cromwell workflow job — cromwell_call","text":"workflow_id (character) single workflow ID","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_call.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Retrieve metadata for the calls made in a Cromwell workflow job — cromwell_call","text":"Returns long form data frame metadata calls. NOTE: currently support subWorkflows well yet.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_call.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Retrieve metadata for the calls made in a Cromwell workflow job — cromwell_call","text":"Now supports nested scatters.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_call.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Retrieve metadata for the calls made in a Cromwell workflow job — cromwell_call","text":"Requires valid Cromwell server URL set. See cromwellSettings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_call.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Retrieve metadata for the calls made in a Cromwell workflow job — cromwell_call","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_call.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Retrieve metadata for the calls made in a Cromwell workflow job — cromwell_call","text":"","code":"if (FALSE) { ## Request what jobs have been submitted to your Cromwell instance in the ## past 7 days. recentJobs <- cromwell_jobs(days = 7) ## Request workflow metadata for a specific job that was run in your ## Cromwell instance. thisWorkflowID <- recentJobs$workflow_id[1] callsMeta <- cromwell_call(workflow_id = thisWorkflowID) }"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_config.html","id":null,"dir":"Reference","previous_headings":"","what":"Cromwell Configuration — cromwell_config","title":"Cromwell Configuration — cromwell_config","text":"Cromwell Configuration","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_config.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Cromwell Configuration — cromwell_config","text":"","code":"cromwell_config(cromwell_url = NULL, verbose = TRUE)"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_config.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Cromwell Configuration — cromwell_config","text":"cromwell_url (character) Cromwell server URL. full url, example \"http://localhost:8000\" \"https://mycromwell.com\" verbose (logical) verbose messaging. default: TRUE. toggles (TRUE) (FALSE) messages throughout package.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_config.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Cromwell Configuration — cromwell_config","text":"Note although default value cromwell_url NULL, fetch current value CROMWELLURL env var internally cromwell_url=NULL - thus, retain value CROMWELLURL set even function run without passing anything cromwell_url","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_config.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Cromwell Configuration — cromwell_config","text":"Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_config.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Cromwell Configuration — cromwell_config","text":"","code":"if (FALSE) { cromwell_config() cromwell_config(\"https://mycromwellinstance.com\") cromwell_config(verbose = FALSE) }"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_failures.html","id":null,"dir":"Reference","previous_headings":"","what":"Pull metadata for the failed calls made in a Cromwell workflow job — cromwell_failures","title":"Pull metadata for the failed calls made in a Cromwell workflow job — cromwell_failures","text":"Gets info failed calls specific workflow","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_failures.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pull metadata for the failed calls made in a Cromwell workflow job — cromwell_failures","text":"","code":"cromwell_failures(workflow_id)"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_failures.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pull metadata for the failed calls made in a Cromwell workflow job — cromwell_failures","text":"workflow_id (character) single workflow ID","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_failures.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pull metadata for the failed calls made in a Cromwell workflow job — cromwell_failures","text":"Returns long form data frame metadata failed calls workflow.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_failures.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Pull metadata for the failed calls made in a Cromwell workflow job — cromwell_failures","text":"Requires valid Cromwell server URL set. See cromwellSettings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_failures.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Pull metadata for the failed calls made in a Cromwell workflow job — cromwell_failures","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_failures.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Pull metadata for the failed calls made in a Cromwell workflow job — cromwell_failures","text":"","code":"if (FALSE) { ## Request what jobs have been submitted to your Cromwell instance in the ## past 7 days. recentJobs <- cromwell_jobs(days = 7) ## Request workflow metadata for a specific job that was run in your ## Cromwell instance. thisWorkflowID <- recentJobs$workflow_id[1] failsMeta <- cromwell_failures(workflow_id = thisWorkflowID) }"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_glob.html","id":null,"dir":"Reference","previous_headings":"","what":"Pull a glob of metadata for a specific Cromwell workflow job — cromwell_glob","title":"Pull a glob of metadata for a specific Cromwell workflow job — cromwell_glob","text":"Retrieve glob workflow level metadata specific workflow.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_glob.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pull a glob of metadata for a specific Cromwell workflow job — cromwell_glob","text":"","code":"cromwell_glob(workflow_id, expand_sub_workflows = FALSE)"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_glob.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pull a glob of metadata for a specific Cromwell workflow job — cromwell_glob","text":"workflow_id (character) single workflow ID expand_sub_workflows Boolean, whether expand subworkflows results , default FALSE.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_glob.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pull a glob of metadata for a specific Cromwell workflow job — cromwell_glob","text":"Returns gross list lists metadata workflow.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_glob.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Pull a glob of metadata for a specific Cromwell workflow job — cromwell_glob","text":"Requires valid Cromwell server URL set. See cromwellSettings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_glob.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Pull a glob of metadata for a specific Cromwell workflow job — cromwell_glob","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_glob.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Pull a glob of metadata for a specific Cromwell workflow job — cromwell_glob","text":"","code":"if (FALSE) { ## Request what jobs have been submitted to your Cromwell instance in the ## past 7 days. recentJobs <- cromwell_jobs(days = 7) ## Request workflow metadata for a specific job that was run in your ## Cromwell instance. thisWorkflowID <- recentJobs$workflow_id[1] workflowMeta <- cromwell_glob(workflow_id = thisWorkflowID) }"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_jobs.html","id":null,"dir":"Reference","previous_headings":"","what":"Requests metadata about Cromwell workflow jobs during a time period specified — cromwell_jobs","title":"Requests metadata about Cromwell workflow jobs during a time period specified — cromwell_jobs","text":"Requests metadata Cromwell workflow jobs time period specified","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_jobs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Requests metadata about Cromwell workflow jobs during a time period specified — cromwell_jobs","text":"","code":"cromwell_jobs(days = 1, workflow_name = NULL, workflow_status = NULL)"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_jobs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Requests metadata about Cromwell workflow jobs during a time period specified — cromwell_jobs","text":"days number days history return, defaults 1 day. workflow_name array strings valid workflow names want job list. workflow_status array strings valid workflow statuses want job list (e.g., submitted, running, succeeded, failed, aborting, aborted)","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_jobs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Requests metadata about Cromwell workflow jobs during a time period specified — cromwell_jobs","text":"Returns long form data frame metadata workflow jobs submitted specific Cromwell instance.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_jobs.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Requests metadata about Cromwell workflow jobs during a time period specified — cromwell_jobs","text":"Requires valid Cromwell server URL set. See cromwellSettings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_jobs.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Requests metadata about Cromwell workflow jobs during a time period specified — cromwell_jobs","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_jobs.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Requests metadata about Cromwell workflow jobs during a time period specified — cromwell_jobs","text":"","code":"if (FALSE) { ## Request what jobs have been submitted to your Cromwell instance in the ## past 7 days. recentJobs <- cromwell_jobs(days = 7) }"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_logs.html","id":null,"dir":"Reference","previous_headings":"","what":"Gets logs for a workflow in Cromwell — cromwell_logs","title":"Gets logs for a workflow in Cromwell — cromwell_logs","text":"Gets logs workflow Cromwell","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_logs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Gets logs for a workflow in Cromwell — cromwell_logs","text":"","code":"cromwell_logs(workflow_id)"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_logs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Gets logs for a workflow in Cromwell — cromwell_logs","text":"workflow_id (character) single workflow ID","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_logs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Gets logs for a workflow in Cromwell — cromwell_logs","text":"Returns response API post","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_logs.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Gets logs for a workflow in Cromwell — cromwell_logs","text":"Requires valid Cromwell server URL set. See cromwellSettings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_logs.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Gets logs for a workflow in Cromwell — cromwell_logs","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_outputs.html","id":null,"dir":"Reference","previous_headings":"","what":"Gets outputs for a workflow in Cromwell — cromwell_outputs","title":"Gets outputs for a workflow in Cromwell — cromwell_outputs","text":"Gets outputs workflow Cromwell","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_outputs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Gets outputs for a workflow in Cromwell — cromwell_outputs","text":"","code":"cromwell_outputs(workflow_id)"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_outputs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Gets outputs for a workflow in Cromwell — cromwell_outputs","text":"workflow_id (character) single workflow ID","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_outputs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Gets outputs for a workflow in Cromwell — cromwell_outputs","text":"Returns dataframe containing workflowName, workflowOutputType, pathToOutput, shardIndex specified outputs workflow_id","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_outputs.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Gets outputs for a workflow in Cromwell — cromwell_outputs","text":"Requires valid Cromwell server URL set. See cromwellSettings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_outputs.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Gets outputs for a workflow in Cromwell — cromwell_outputs","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_submit_batch.html","id":null,"dir":"Reference","previous_headings":"","what":"Submit a workflow job to Cromwell — cromwell_submit_batch","title":"Submit a workflow job to Cromwell — cromwell_submit_batch","text":"Supports submission fully defined workflow job Cromwell instance.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_submit_batch.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Submit a workflow job to Cromwell — cromwell_submit_batch","text":"","code":"cromwell_submit_batch(   wdl,   batch = NULL,   params = NULL,   options = NULL,   labels = NULL,   dependencies = NULL )"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_submit_batch.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Submit a workflow job to Cromwell — cromwell_submit_batch","text":"wdl Local path wdl file describing workflow. (Required) batch Local path json containing reference batch file desired workflow batch. (Optional) params Local path json containing parameters use workflow. (Optional) options Local path json containing workflow options apply. (Optional) labels data frame containing labels workflow. (Optional) dependencies zip'd file subworkflow dependencies. (Optional)","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_submit_batch.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Submit a workflow job to Cromwell — cromwell_submit_batch","text":"Returns response API post includes workflow ID need monitor job.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_submit_batch.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Submit a workflow job to Cromwell — cromwell_submit_batch","text":"Requires valid Cromwell server URL set. See cromwellSettings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_submit_batch.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Submit a workflow job to Cromwell — cromwell_submit_batch","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_timing.html","id":null,"dir":"Reference","previous_headings":"","what":"Get a timing diagram for a Cromwell workflow — cromwell_timing","title":"Get a timing diagram for a Cromwell workflow — cromwell_timing","text":"Get timing diagram Cromwell workflow","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_timing.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get a timing diagram for a Cromwell workflow — cromwell_timing","text":"","code":"cromwell_timing(workflow_id)"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_timing.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get a timing diagram for a Cromwell workflow — cromwell_timing","text":"workflow_id (character) single workflow ID","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_timing.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get a timing diagram for a Cromwell workflow — cromwell_timing","text":"Opens timing diagram browser","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_timing.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Get a timing diagram for a Cromwell workflow — cromwell_timing","text":"Requires valid Cromwell server URL set. See cromwellSettings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_timing.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Get a timing diagram for a Cromwell workflow — cromwell_timing","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_validate.html","id":null,"dir":"Reference","previous_headings":"","what":"Validates a workflow for submission — cromwell_validate","title":"Validates a workflow for submission — cromwell_validate","text":"Validates workflow submission","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_validate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Validates a workflow for submission — cromwell_validate","text":"","code":"cromwell_validate(wdl, all_inputs = NULL)"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_validate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Validates a workflow for submission — cromwell_validate","text":"wdl Local path wdl file describing workflow. (Required) all_inputs Local path json containing inputs parameters use workflow - batch parameters json present must first combined. (Optional)","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_validate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Validates a workflow for submission — cromwell_validate","text":"Returns response API post includes workflow ID need monitor job.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_validate.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Validates a workflow for submission — cromwell_validate","text":"Requires valid Cromwell server URL set. See cromwellSettings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_validate.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Validates a workflow for submission — cromwell_validate","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_version.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the version of a Cromwell server — cromwell_version","title":"Get the version of a Cromwell server — cromwell_version","text":"Get version Cromwell server","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_version.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the version of a Cromwell server — cromwell_version","text":"","code":"cromwell_version()"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_version.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get the version of a Cromwell server — cromwell_version","text":"(character) Cromwell version","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_version.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Get the version of a Cromwell server — cromwell_version","text":"Requires valid Cromwell server URL set. See cromwellSettings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_version.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Get the version of a Cromwell server — cromwell_version","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_workflow.html","id":null,"dir":"Reference","previous_headings":"","what":"Pull metadata for a specific Cromwell workflow job — cromwell_workflow","title":"Pull metadata for a specific Cromwell workflow job — cromwell_workflow","text":"Retrieve process labels, submission workflow level metadata specific workflow.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_workflow.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pull metadata for a specific Cromwell workflow job — cromwell_workflow","text":"","code":"cromwell_workflow(workflow_id)"},{"path":"http://getwilds.org/rcromwell/reference/cromwell_workflow.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pull metadata for a specific Cromwell workflow job — cromwell_workflow","text":"workflow_id (character) single workflow ID","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_workflow.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pull metadata for a specific Cromwell workflow job — cromwell_workflow","text":"Returns long form data frame metadata workflow.","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_workflow.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Pull metadata for a specific Cromwell workflow job — cromwell_workflow","text":"Requires valid Cromwell server URL set. See cromwellSettings","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_workflow.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Pull metadata for a specific Cromwell workflow job — cromwell_workflow","text":"Amy Paguirigan","code":""},{"path":"http://getwilds.org/rcromwell/reference/cromwell_workflow.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Pull metadata for a specific Cromwell workflow job — cromwell_workflow","text":"","code":"if (FALSE) { ## Request what jobs have been submitted to your Cromwell instance in the ## past 7 days. recentJobs <- cromwell_jobs(days = 7) ## Request workflow metadata for a specific job that was run in your ## Cromwell instance. thisWorkflowID <- recentJobs$workflow_id[1] workflowMeta <- cromwell_workflow(workflow_id = thisWorkflowID) }"},{"path":"http://getwilds.org/rcromwell/reference/rcromwell-package.html","id":null,"dir":"Reference","previous_headings":"","what":"rcromwell: Convenience Tools for Managing WDL Workflows via Cromwell — rcromwell-package","title":"rcromwell: Convenience Tools for Managing WDL Workflows via Cromwell — rcromwell-package","text":"repo containing basic R package using Cromwell WDL workflows via R.","code":""},{"path":[]},{"path":"http://getwilds.org/rcromwell/reference/rcromwell-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"rcromwell: Convenience Tools for Managing WDL Workflows via Cromwell — rcromwell-package","text":"Maintainer: Scott Chamberlain sachamber@fredhutch.org (ORCID) Authors: Amy Paguirigan (ORCID)","code":""},{"path":"http://getwilds.org/rcromwell/reference/workflow_inputs.html","id":null,"dir":"Reference","previous_headings":"","what":"Pull the workflow inputs provided for a Cromwell workflow job — workflow_inputs","title":"Pull the workflow inputs provided for a Cromwell workflow job — workflow_inputs","text":"Pull workflow inputs provided Cromwell workflow job","code":""},{"path":"http://getwilds.org/rcromwell/reference/workflow_inputs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pull the workflow inputs provided for a Cromwell workflow job — workflow_inputs","text":"","code":"workflow_inputs(workflow_id)"},{"path":"http://getwilds.org/rcromwell/reference/workflow_inputs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pull the workflow inputs provided for a Cromwell workflow job — workflow_inputs","text":"workflow_id (character) single workflow ID","code":""},{"path":"http://getwilds.org/rcromwell/reference/workflow_inputs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pull the workflow inputs provided for a Cromwell workflow job — workflow_inputs","text":"Returns data frame inputs workflow previously run","code":""},{"path":"http://getwilds.org/rcromwell/reference/workflow_inputs.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Pull the workflow inputs provided for a Cromwell workflow job — workflow_inputs","text":"Requires valid Cromwell server URL set. See cromwellSettings","code":""},{"path":"http://getwilds.org/rcromwell/reference/workflow_inputs.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Pull the workflow inputs provided for a Cromwell workflow job — workflow_inputs","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/workflow_options.html","id":null,"dir":"Reference","previous_headings":"","what":"Pull the workflow options provided for a Cromwell workflow job — workflow_options","title":"Pull the workflow options provided for a Cromwell workflow job — workflow_options","text":"Pull workflow options provided Cromwell workflow job","code":""},{"path":"http://getwilds.org/rcromwell/reference/workflow_options.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pull the workflow options provided for a Cromwell workflow job — workflow_options","text":"","code":"workflow_options(workflow_id)"},{"path":"http://getwilds.org/rcromwell/reference/workflow_options.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pull the workflow options provided for a Cromwell workflow job — workflow_options","text":"workflow_id (character) single workflow ID","code":""},{"path":"http://getwilds.org/rcromwell/reference/workflow_options.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pull the workflow options provided for a Cromwell workflow job — workflow_options","text":"Returns data frame options workflow previously run","code":""},{"path":"http://getwilds.org/rcromwell/reference/workflow_options.html","id":"important","dir":"Reference","previous_headings":"","what":"Important","title":"Pull the workflow options provided for a Cromwell workflow job — workflow_options","text":"Requires valid Cromwell server URL set. See cromwellSettings","code":""},{"path":"http://getwilds.org/rcromwell/reference/workflow_options.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Pull the workflow options provided for a Cromwell workflow job — workflow_options","text":"Amy Paguirigan, Scott Chamberlain","code":""},{"path":"http://getwilds.org/rcromwell/reference/workflow_options.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Pull the workflow options provided for a Cromwell workflow job — workflow_options","text":"","code":"if (FALSE) { jobs <- cromwell_jobs() workflow_options(jobs$workflow_id[1]) }"},{"path":"http://getwilds.org/rcromwell/news/index.html","id":"rcromwell-300","dir":"Changelog","previous_headings":"","what":"rcromwell 3.0.0","title":"rcromwell 3.0.0","text":"First version package new name rcromwell Functions functions arguments changed camelCase snake_case Package now tests Package documentation added http://getwilds.org/rcromwell/","code":""}]
diff --git a/sitemap.xml b/sitemap.xml
index 73ac637..94b7d84 100644
--- a/sitemap.xml
+++ b/sitemap.xml
@@ -3,6 +3,9 @@
   <url>
     <loc>http://getwilds.org/rcromwell/404.html</loc>
   </url>
+  <url>
+    <loc>http://getwilds.org/rcromwell/CODE_OF_CONDUCT.html</loc>
+  </url>
   <url>
     <loc>http://getwilds.org/rcromwell/LICENSE-text.html</loc>
   </url>
