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hds-sandbox · Aug 20, 2024 · 6298692 · 6298692
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diff --git a/.nojekyll b/.nojekyll
@@ -1 +1 @@
-1f7e2651
+bf1f7a9e
diff --git a/about/about.html b/about/about.html
@@ -2,12 +2,12 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.557">
+<meta name="generator" content="quarto-1.5.56">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
 
-<title>Introduction to NGS data analysis - About the Sandbox</title>
+<title>About the Sandbox – Introduction to NGS data analysis</title>
 <style>
 code{white-space: pre-wrap;}
 span.smallcaps{font-variant: small-caps;}
@@ -80,7 +80,7 @@
 <script type="application/ld+json">
   {
     "@context": "https://schema.org/",
-    "@type": "LearningResource",
+    "@type": "TrainingMaterial",
     "@id": "https://hds-sandbox.github.io/NGS_summer_course_Aarhus/",
     "dct:conformsTo": {
       "http://purl.org/dc/terms/conformsTo": {
@@ -171,7 +171,7 @@
 </script>
 
 
-<meta property="og:title" content="Introduction to NGS data analysis - About the Sandbox">
+<meta property="og:title" content="About the Sandbox – Introduction to NGS data analysis">
 <meta property="og:description" content="">
 <meta property="og:site_name" content="Introduction to NGS data analysis">
 <meta property="og:locale" content="en_US">
@@ -192,7 +192,7 @@
     </a>
   </div>
             <div id="quarto-search" class="" title="Search"></div>
-          <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbarCollapse" aria-controls="navbarCollapse" aria-expanded="false" aria-label="Toggle navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
+          <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbarCollapse" aria-controls="navbarCollapse" role="menu" aria-expanded="false" aria-label="Toggle navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
   <span class="navbar-toggler-icon"></span>
 </button>
           <div class="collapse navbar-collapse" id="navbarCollapse">
@@ -206,11 +206,15 @@
 <span class="menu-text">Slides</span></a>
   </li>  
   <li class="nav-item dropdown ">
-    <a class="nav-link dropdown-toggle" href="#" id="nav-menu-access" role="button" data-bs-toggle="dropdown" aria-expanded="false">
+    <a class="nav-link dropdown-toggle" href="#" id="nav-menu-access" role="link" data-bs-toggle="dropdown" aria-expanded="false">
  <span class="menu-text">Access</span>
     </a>
     <ul class="dropdown-menu" aria-labelledby="nav-menu-access">    
         <li>
+    <a class="dropdown-item" href="../access/ngssummer.html">
+ <span class="dropdown-text">Summer School</span></a>
+  </li>  
+        <li>
     <a class="dropdown-item" href="../access/UCloud.html">
  <span class="dropdown-text">UCloud</span></a>
   </li>  
@@ -221,7 +225,7 @@
     </ul>
   </li>
   <li class="nav-item dropdown ">
-    <a class="nav-link dropdown-toggle" href="#" id="nav-menu-tutorials" role="button" data-bs-toggle="dropdown" aria-expanded="false">
+    <a class="nav-link dropdown-toggle" href="#" id="nav-menu-tutorials" role="link" data-bs-toggle="dropdown" aria-expanded="false">
  <span class="menu-text">Tutorials</span>
     </a>
     <ul class="dropdown-menu" aria-labelledby="nav-menu-tutorials">    
@@ -256,7 +260,7 @@
   </li>  
 </ul>
           </div> <!-- /navcollapse -->
-          <div class="quarto-navbar-tools">
+            <div class="quarto-navbar-tools">
   <a href="" class="quarto-color-scheme-toggle quarto-navigation-tool  px-1" onclick="window.quartoToggleColorScheme(); return false;" title="Toggle dark mode"><i class="bi"></i></a>
 </div>
       </div> <!-- /container-fluid -->
@@ -502,18 +506,7 @@ <h1>Partner with the Sandbox</h1>
     }
     return false;
   }
-  const clipboard = new window.ClipboardJS('.code-copy-button', {
-    text: function(trigger) {
-      const codeEl = trigger.previousElementSibling.cloneNode(true);
-      for (const childEl of codeEl.children) {
-        if (isCodeAnnotation(childEl)) {
-          childEl.remove();
-        }
-      }
-      return codeEl.innerText;
-    }
-  });
-  clipboard.on('success', function(e) {
+  const onCopySuccess = function(e) {
     // button target
     const button = e.trigger;
     // don't keep focus
@@ -545,15 +538,37 @@ <h1>Partner with the Sandbox</h1>
     }, 1000);
     // clear code selection
     e.clearSelection();
+  }
+  const getTextToCopy = function(trigger) {
+      const codeEl = trigger.previousElementSibling.cloneNode(true);
+      for (const childEl of codeEl.children) {
+        if (isCodeAnnotation(childEl)) {
+          childEl.remove();
+        }
+      }
+      return codeEl.innerText;
+  }
+  const clipboard = new window.ClipboardJS('.code-copy-button:not([data-in-quarto-modal])', {
+    text: getTextToCopy
   });
+  clipboard.on('success', onCopySuccess);
+  if (window.document.getElementById('quarto-embedded-source-code-modal')) {
+    // For code content inside modals, clipBoardJS needs to be initialized with a container option
+    // TODO: Check when it could be a function (https://github.com/zenorocha/clipboard.js/issues/860)
+    const clipboardModal = new window.ClipboardJS('.code-copy-button[data-in-quarto-modal]', {
+      text: getTextToCopy,
+      container: window.document.getElementById('quarto-embedded-source-code-modal')
+    });
+    clipboardModal.on('success', onCopySuccess);
+  }
     var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
     var mailtoRegex = new RegExp(/^mailto:/);
       var filterRegex = new RegExp("https:\/\/hds-sandbox\.github\.io\/NGS_summer_course_Aarhus\/");
     var isInternal = (href) => {
         return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href);
     }
     // Inspect non-navigation links and adorn them if external
- 	var links = window.document.querySelectorAll('a[href]:not(.nav-link):not(.navbar-brand):not(.toc-action):not(.sidebar-link):not(.sidebar-item-toggle):not(.pagination-link):not(.no-external):not([aria-hidden]):not(.dropdown-item):not(.quarto-navigation-tool)');
+ 	var links = window.document.querySelectorAll('a[href]:not(.nav-link):not(.navbar-brand):not(.toc-action):not(.sidebar-link):not(.sidebar-item-toggle):not(.pagination-link):not(.no-external):not([aria-hidden]):not(.dropdown-item):not(.quarto-navigation-tool):not(.about-link)');
     for (var i=0; i<links.length; i++) {
       const link = links[i];
       if (!isInternal(link.href)) {

diff --git a/access/UCloud.html b/access/UCloud.html
@@ -2,12 +2,12 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.557">
+<meta name="generator" content="quarto-1.5.56">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
 
-<title>Introduction to NGS data analysis - Accessing the NGS summer school on UCloud</title>
+<title>Accessing the NGS summer school on UCloud – Introduction to NGS data analysis</title>
 <style>
 code{white-space: pre-wrap;}
 span.smallcaps{font-variant: small-caps;}
@@ -80,7 +80,7 @@
 <script type="application/ld+json">
   {
     "@context": "https://schema.org/",
-    "@type": "LearningResource",
+    "@type": "TrainingMaterial",
     "@id": "https://hds-sandbox.github.io/NGS_summer_course_Aarhus/",
     "dct:conformsTo": {
       "http://purl.org/dc/terms/conformsTo": {
@@ -171,7 +171,7 @@
 </script>
 
 
-<meta property="og:title" content="Introduction to NGS data analysis - Accessing the NGS summer school on UCloud">
+<meta property="og:title" content="Accessing the NGS summer school on UCloud – Introduction to NGS data analysis">
 <meta property="og:description" content="">
 <meta property="og:image" content="https://hds-sandbox.github.io/NGS_summer_course_Aarhus/images/recoverJobs.gif">
 <meta property="og:site_name" content="Introduction to NGS data analysis">
@@ -193,7 +193,7 @@
     </a>
   </div>
             <div id="quarto-search" class="" title="Search"></div>
-          <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbarCollapse" aria-controls="navbarCollapse" aria-expanded="false" aria-label="Toggle navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
+          <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbarCollapse" aria-controls="navbarCollapse" role="menu" aria-expanded="false" aria-label="Toggle navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
   <span class="navbar-toggler-icon"></span>
 </button>
           <div class="collapse navbar-collapse" id="navbarCollapse">
@@ -207,11 +207,15 @@
 <span class="menu-text">Slides</span></a>
   </li>  
   <li class="nav-item dropdown ">
-    <a class="nav-link dropdown-toggle" href="#" id="nav-menu-access" role="button" data-bs-toggle="dropdown" aria-expanded="false">
+    <a class="nav-link dropdown-toggle" href="#" id="nav-menu-access" role="link" data-bs-toggle="dropdown" aria-expanded="false">
  <span class="menu-text">Access</span>
     </a>
     <ul class="dropdown-menu" aria-labelledby="nav-menu-access">    
         <li>
+    <a class="dropdown-item" href="../access/ngssummer.html">
+ <span class="dropdown-text">Summer School</span></a>
+  </li>  
+        <li>
     <a class="dropdown-item" href="../access/UCloud.html">
  <span class="dropdown-text">UCloud</span></a>
   </li>  
@@ -222,7 +226,7 @@
     </ul>
   </li>
   <li class="nav-item dropdown ">
-    <a class="nav-link dropdown-toggle" href="#" id="nav-menu-tutorials" role="button" data-bs-toggle="dropdown" aria-expanded="false">
+    <a class="nav-link dropdown-toggle" href="#" id="nav-menu-tutorials" role="link" data-bs-toggle="dropdown" aria-expanded="false">
  <span class="menu-text">Tutorials</span>
     </a>
     <ul class="dropdown-menu" aria-labelledby="nav-menu-tutorials">    
@@ -257,7 +261,7 @@
   </li>  
 </ul>
           </div> <!-- /navcollapse -->
-          <div class="quarto-navbar-tools">
+            <div class="quarto-navbar-tools">
   <a href="" class="quarto-color-scheme-toggle quarto-navigation-tool  px-1" onclick="window.quartoToggleColorScheme(); return false;" title="Toggle dark mode"><i class="bi"></i></a>
 </div>
       </div> <!-- /container-fluid -->
@@ -566,18 +570,7 @@ <h1>Recovering the material from your previous session</h1>
     }
     return false;
   }
-  const clipboard = new window.ClipboardJS('.code-copy-button', {
-    text: function(trigger) {
-      const codeEl = trigger.previousElementSibling.cloneNode(true);
-      for (const childEl of codeEl.children) {
-        if (isCodeAnnotation(childEl)) {
-          childEl.remove();
-        }
-      }
-      return codeEl.innerText;
-    }
-  });
-  clipboard.on('success', function(e) {
+  const onCopySuccess = function(e) {
     // button target
     const button = e.trigger;
     // don't keep focus
@@ -609,15 +602,37 @@ <h1>Recovering the material from your previous session</h1>
     }, 1000);
     // clear code selection
     e.clearSelection();
+  }
+  const getTextToCopy = function(trigger) {
+      const codeEl = trigger.previousElementSibling.cloneNode(true);
+      for (const childEl of codeEl.children) {
+        if (isCodeAnnotation(childEl)) {
+          childEl.remove();
+        }
+      }
+      return codeEl.innerText;
+  }
+  const clipboard = new window.ClipboardJS('.code-copy-button:not([data-in-quarto-modal])', {
+    text: getTextToCopy
   });
+  clipboard.on('success', onCopySuccess);
+  if (window.document.getElementById('quarto-embedded-source-code-modal')) {
+    // For code content inside modals, clipBoardJS needs to be initialized with a container option
+    // TODO: Check when it could be a function (https://github.com/zenorocha/clipboard.js/issues/860)
+    const clipboardModal = new window.ClipboardJS('.code-copy-button[data-in-quarto-modal]', {
+      text: getTextToCopy,
+      container: window.document.getElementById('quarto-embedded-source-code-modal')
+    });
+    clipboardModal.on('success', onCopySuccess);
+  }
     var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
     var mailtoRegex = new RegExp(/^mailto:/);
       var filterRegex = new RegExp("https:\/\/hds-sandbox\.github\.io\/NGS_summer_course_Aarhus\/");
     var isInternal = (href) => {
         return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href);
     }
     // Inspect non-navigation links and adorn them if external
- 	var links = window.document.querySelectorAll('a[href]:not(.nav-link):not(.navbar-brand):not(.toc-action):not(.sidebar-link):not(.sidebar-item-toggle):not(.pagination-link):not(.no-external):not([aria-hidden]):not(.dropdown-item):not(.quarto-navigation-tool)');
+ 	var links = window.document.querySelectorAll('a[href]:not(.nav-link):not(.navbar-brand):not(.toc-action):not(.sidebar-link):not(.sidebar-item-toggle):not(.pagination-link):not(.no-external):not([aria-hidden]):not(.dropdown-item):not(.quarto-navigation-tool):not(.about-link)');
     for (var i=0; i<links.length; i++) {
       const link = links[i];
       if (!isInternal(link.href)) {