Deployed 4fbb73e to main with MkDocs 1.6.1 and mike 2.1.3

main/404.html

@@ -16,7 +16,7 @@
 
 
       <link rel="icon" href="/public_health_bioinformatics/main/assets/logos/Theiagen-Symbol-Standard-01.png">
-      <meta name="generator" content="mkdocs-1.6.1, mkdocs-material-9.5.48">
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@@ -4167,7 +4167,7 @@ <h1>404 - Not found</h1>
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main/assets/new_workflow_template/index.html

@@ -18,7 +18,7 @@
 
 
       <link rel="icon" href="../logos/Theiagen-Symbol-Standard-01.png">
-      <meta name="generator" content="mkdocs-1.6.1, mkdocs-material-9.5.48">
+      <meta name="generator" content="mkdocs-1.6.1, mkdocs-material-9.5.49">
 
 
 
@@ -4410,7 +4410,7 @@ <h2 id="references-if-applicable">References (if applicable)<a class="headerlink
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-      <script src="../javascripts/bundle.83f73b43.min.js"></script>
+      <script src="../javascripts/bundle.88dd0f4e.min.js"></script>
 
         <script src="https://unpkg.com/[email protected]/dist/tablesort.min.js"></script>
 

main/contributing/code_contribution/index.html

@@ -20,7 +20,7 @@
 
 
       <link rel="icon" href="../../assets/logos/Theiagen-Symbol-Standard-01.png">
-      <meta name="generator" content="mkdocs-1.6.1, mkdocs-material-9.5.48">
+      <meta name="generator" content="mkdocs-1.6.1, mkdocs-material-9.5.49">
 
 
 
@@ -4885,7 +4885,7 @@ <h2 id="example-workflow-formats">Example Workflow formats<a class="headerlink"
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-      <script src="../../assets/javascripts/bundle.83f73b43.min.js"></script>
+      <script src="../../assets/javascripts/bundle.88dd0f4e.min.js"></script>
 
         <script src="https://unpkg.com/[email protected]/dist/tablesort.min.js"></script>
 

main/contributing/doc_contribution/index.html

@@ -22,7 +22,7 @@
 
 
       <link rel="icon" href="../../assets/logos/Theiagen-Symbol-Standard-01.png">
-      <meta name="generator" content="mkdocs-1.6.1, mkdocs-material-9.5.48">
+      <meta name="generator" content="mkdocs-1.6.1, mkdocs-material-9.5.49">
 
 
 
@@ -4674,7 +4674,7 @@ <h3 id="new-page">Adding a Page for a New Workflow<a class="headerlink" href="#n
     <script id="__config" type="application/json">{"base": "../..", "features": ["content.code.annotate", "content.code.copy", "content.tabs.link", "content.tooltips", "navigation.instant", "navigation.path", "navigation.tabs", "navigation.top", "navigation.tracking", "search.highlight", "search.suggest", "toc.follow"], "search": "../../assets/javascripts/workers/search.6ce7567c.min.js", "translations": {"clipboard.copied": "Copied to clipboard", "clipboard.copy": "Copy to clipboard", "search.result.more.one": "1 more on this page", "search.result.more.other": "# more on this page", "search.result.none": "No matching documents", "search.result.one": "1 matching document", "search.result.other": "# matching documents", "search.result.placeholder": "Type to start searching", "search.result.term.missing": "Missing", "select.version": "Select version"}, "version": {"alias": true, "default": "latest", "provider": "mike"}}</script>
 
 
-      <script src="../../assets/javascripts/bundle.83f73b43.min.js"></script>
+      <script src="../../assets/javascripts/bundle.88dd0f4e.min.js"></script>
 
         <script src="https://unpkg.com/[email protected]/dist/tablesort.min.js"></script>
 

main/getting_started/commandline/index.html

@@ -22,7 +22,7 @@
 
 
       <link rel="icon" href="../../assets/logos/Theiagen-Symbol-Standard-01.png">
-      <meta name="generator" content="mkdocs-1.6.1, mkdocs-material-9.5.48">
+      <meta name="generator" content="mkdocs-1.6.1, mkdocs-material-9.5.49">
 
 
 
@@ -4840,7 +4840,7 @@ <h2 id="step-7-troubleshooting-and-debugging">Step 7: Troubleshooting and Debugg
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-      <script src="../../assets/javascripts/bundle.83f73b43.min.js"></script>
+      <script src="../../assets/javascripts/bundle.88dd0f4e.min.js"></script>
 
         <script src="https://unpkg.com/[email protected]/dist/tablesort.min.js"></script>
 

main/getting_started/terra/index.html

@@ -22,7 +22,7 @@
 
 
       <link rel="icon" href="../../assets/logos/Theiagen-Symbol-Standard-01.png">
-      <meta name="generator" content="mkdocs-1.6.1, mkdocs-material-9.5.48">
+      <meta name="generator" content="mkdocs-1.6.1, mkdocs-material-9.5.49">
 
 
 
@@ -4703,7 +4703,7 @@ <h2 id="sars-cov-2-metagenomic-analysis">SARS-CoV-2 Metagenomic Analysis<a class
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-      <script src="../../assets/javascripts/bundle.83f73b43.min.js"></script>
+      <script src="../../assets/javascripts/bundle.88dd0f4e.min.js"></script>
 
         <script src="https://unpkg.com/[email protected]/dist/tablesort.min.js"></script>
 

main/index.html

@@ -20,7 +20,7 @@
 
 
       <link rel="icon" href="assets/logos/Theiagen-Symbol-Standard-01.png">
-      <meta name="generator" content="mkdocs-1.6.1, mkdocs-material-9.5.48">
+      <meta name="generator" content="mkdocs-1.6.1, mkdocs-material-9.5.49">
 
 
 
@@ -4431,7 +4431,7 @@ <h3 id="phb-development-is-a-cycle">PHB development is a cycle<a class="headerli
 <p>We continuously work to improve our codebase and usability of our workflows by the public health community, so changes from version to version are expected.  This documentation page reflects the state of the workflow at the version stated in the title.</p>
 <div class="admonition dna">
 <p class="admonition-title">What's new?</p>
-<p>You can see the changes since PHB v2.2.0 <a href="https://theiagen.notion.site/Public-Health-Bioinformatics-v2-2-1-Patch-Release-Notes-104cb013bc9380bcbd70dab04bf671a8?pvs=74"><strong>here</strong></a>!</p>
+<p>You can see the changes since PHB v2.2.1 <a href="https://theiagen.notion.site/public-health-bioinformatics-v2-3-0-minor-release-notes?pvs=4"><strong>here</strong></a>!</p>
 </div>
 <h2 id="contributing-to-the-phb-repository">Contributing to the PHB Repository<a class="headerlink" href="#contributing-to-the-phb-repository" title="Permanent link">&para;</a></h2>
 <p>We warmly welcome contributions to this repository! Our style guide may be found <a href="contributing/code_contribution/">here</a> for convenience of formatting.</p>
@@ -4452,7 +4452,6 @@ <h3 id="authorship">Authorship<a class="headerlink" href="#authorship" title="Pe
 <li><strong>Michal Babinski</strong> (<a href="https://github.com/Michal-Babins">@Michal-Babins</a>) - Software, Validation</li>
 <li><strong>Andrew Lang</strong> (<a href="https://github.com/AndrewLangVt">@AndrewLangVt</a>) - Software, Supervision</li>
 <li><strong>Kelsey Kropp</strong> (<a href="https://github.com/kelseykropp">@kelseykropp</a>) - Validation</li>
-<li><strong>Emily Smith</strong> (<a href="https://github.com/emily-smith1">@emily-smith1</a>) - Validation</li>
 <li><strong>Joel Sevinsky</strong> (<a href="https://github.com/sevinsky">@sevinsky</a>) - Conceptualization, Project Administration, Supervision</li>
 </ul>
 <h3 id="external-contributors">External Contributors<a class="headerlink" href="#external-contributors" title="Permanent link">&para;</a></h3>
@@ -4464,6 +4463,7 @@ <h3 id="external-contributors">External Contributors<a class="headerlink" href="
 <li><strong>Ash O'Farrel</strong> (<a href="https://github.com/aofarrel">@aofarrel</a>)</li>
 <li><strong>Sam Baird</strong> (<a href="https://github.com/sam-baird">@sam-baird</a>)</li>
 <li><strong>Holly Halstead</strong> (<a href="https://github.com/HNHalstead">@HNHalstead</a>)</li>
+<li><strong>Emily Smith</strong> (<a href="https://github.com/emily-smith1">@emily-smith1</a>)</li>
 </ul>
 <h3 id="on-the-shoulder-of-giants">On the Shoulder of Giants<a class="headerlink" href="#on-the-shoulder-of-giants" title="Permanent link">&para;</a></h3>
 <p>The PHB repository would not be possible without its predecessors. We would like to acknowledge the following repositories, individuals, and contributors for their influence on the development of these workflows:</p>
@@ -4508,7 +4508,7 @@ <h2 id="about-theiagen">About Theiagen<a class="headerlink" href="#about-theiage
     <span class="md-icon" title="Last update">
       <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24"><path d="M21 13.1c-.1 0-.3.1-.4.2l-1 1 2.1 2.1 1-1c.2-.2.2-.6 0-.8l-1.3-1.3c-.1-.1-.2-.2-.4-.2m-1.9 1.8-6.1 6V23h2.1l6.1-6.1zM12.5 7v5.2l4 2.4-1 1L11 13V7zM11 21.9c-5.1-.5-9-4.8-9-9.9C2 6.5 6.5 2 12 2c5.3 0 9.6 4.1 10 9.3-.3-.1-.6-.2-1-.2s-.7.1-1 .2C19.6 7.2 16.2 4 12 4c-4.4 0-8 3.6-8 8 0 4.1 3.1 7.5 7.1 7.9l-.1.2z"/></svg>
     </span>
-    <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-12-04</span>
+    <span class="git-revision-date-localized-plugin git-revision-date-localized-plugin-iso_date">2024-12-16</span>
   </span>
 
 
@@ -4617,7 +4617,7 @@ <h2 id="about-theiagen">About Theiagen<a class="headerlink" href="#about-theiage
     <script id="__config" type="application/json">{"base": ".", "features": ["content.code.annotate", "content.code.copy", "content.tabs.link", "content.tooltips", "navigation.instant", "navigation.path", "navigation.tabs", "navigation.top", "navigation.tracking", "search.highlight", "search.suggest", "toc.follow"], "search": "assets/javascripts/workers/search.6ce7567c.min.js", "translations": {"clipboard.copied": "Copied to clipboard", "clipboard.copy": "Copy to clipboard", "search.result.more.one": "1 more on this page", "search.result.more.other": "# more on this page", "search.result.none": "No matching documents", "search.result.one": "1 matching document", "search.result.other": "# matching documents", "search.result.placeholder": "Type to start searching", "search.result.term.missing": "Missing", "select.version": "Select version"}, "version": {"alias": true, "default": "latest", "provider": "mike"}}</script>
 
 
-      <script src="assets/javascripts/bundle.83f73b43.min.js"></script>
+      <script src="assets/javascripts/bundle.88dd0f4e.min.js"></script>
 
         <script src="https://unpkg.com/[email protected]/dist/tablesort.min.js"></script>