From 93761d9fb30e8db4cdd89cb4dc28442c61942191 Mon Sep 17 00:00:00 2001
From: apalleja <apalleja@users.noreply.github.com>
Date: Thu, 24 Oct 2024 08:51:52 +0000
Subject: [PATCH] deploy: dcb0d6a590e4ae03dc079fd4afaa3c561a8202b9

---
 .doctrees/course_contents/Tutorial.doctree    | Bin 0 -> 4403 bytes
 .../course_information/Instructions.doctree   | Bin 6320 -> 7068 bytes
 .doctrees/environment.pickle                  | Bin 28167 -> 28971 bytes
 .doctrees/index.doctree                       | Bin 4442 -> 4476 bytes
 _sources/course_contents/Tutorial.md          |  14 +
 _sources/course_information/Instructions.md   |   8 +-
 _sources/index.md                             |   1 +
 about.html                                    |   1 +
 course_contents/Contents.html                 |   7 +-
 course_contents/Tutorial.html                 | 436 ++++++++++++++++++
 course_information/Instructions.html          |  29 +-
 course_information/Location.html              |   1 +
 course_information/Timing.html                |   1 +
 folder_topic/article_topic.html               |   1 +
 genindex.html                                 |   1 +
 index.html                                    |   1 +
 objects.inv                                   | Bin 402 -> 432 bytes
 resources.html                                |   7 +-
 search.html                                   |   1 +
 searchindex.js                                |   2 +-
 20 files changed, 488 insertions(+), 23 deletions(-)
 create mode 100644 .doctrees/course_contents/Tutorial.doctree
 create mode 100644 _sources/course_contents/Tutorial.md
 create mode 100644 course_contents/Tutorial.html

diff --git a/.doctrees/course_contents/Tutorial.doctree b/.doctrees/course_contents/Tutorial.doctree
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diff --git a/.doctrees/index.doctree b/.doctrees/index.doctree
index 6abf507ce22c22c90510cc1e8d5ad2ca50da2b96..d466b267709ee9012f7ef8fd98e9eae09aecb88b 100644
GIT binary patch
delta 196
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delta 181
zcmeyPbW4e)fpx0?Miv{k$&PGt9Ell0u~RaZB~I>O(`Q^cc?a8E&V7j)A>K?Gp?;GW
zu!;zlW@u+PWyogeWXO4|Wk_dioIIPwm{D!>cJ@z9jDI$-;!<Z}w3&Q~&y3M(GAF+r
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diff --git a/_sources/course_contents/Tutorial.md b/_sources/course_contents/Tutorial.md
new file mode 100644
index 0000000..3179437
--- /dev/null
+++ b/_sources/course_contents/Tutorial.md
@@ -0,0 +1,14 @@
+# Nextflow fundamentals tutorial
+For DTU-Biosustain and DTU-Bioenginnering
+
+Print the current version, system and runtime:
+```bash
+:caption: Verify java installation:
+
+nextflow info
+```
+
+Run hello.nf as it is, passing a parameter from the command line and after changing the code in the second process (rev $y) using –resume
+nextflow run hello.nf
+nextflow run hello.nf --greeting ‘Hello Albert’
+nextflow run hello.nf --greeting ‘Hello Albert’ -resume
diff --git a/_sources/course_information/Instructions.md b/_sources/course_information/Instructions.md
index 6d67fd9..1532cd4 100644
--- a/_sources/course_information/Instructions.md
+++ b/_sources/course_information/Instructions.md
@@ -9,25 +9,25 @@ To learn more about Github codespaces go [here](https://github.com/features/code
 
 Now, Nextflow should be ready to run in your GitHub Codespace environment! Let's check that you have a fully functional environment.
 
-```bash
+```{code-block} bash
 :caption: Verify java installation:
 
 java -version
 ```
 
-```bash
+```{code-block} bash
 :caption: Verify Nextflow installation:
 
 nextflow -v
 ```
 
-```bash
+```{code-block} bash
 :caption: Nextflow information:
 
 nextflow info
 ```
 
-```bash
+```{code-block} bash
 :caption: Verify Docker installation:
 
 docker --version
diff --git a/_sources/index.md b/_sources/index.md
index 952f674..634505d 100644
--- a/_sources/index.md
+++ b/_sources/index.md
@@ -33,6 +33,7 @@ course_information/Timing
 :caption: Course contents
 
 course_contents/Contents
+course_contents/Tutorial
 ```
 
 ```{toctree}
diff --git a/about.html b/about.html
index cb43d26..1afc2c2 100644
--- a/about.html
+++ b/about.html
@@ -172,6 +172,7 @@
 <p aria-level="2" class="caption" role="heading"><span class="caption-text">Course contents</span></p>
 <ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="course_contents/Contents.html">Contents</a></li>
+<li class="toctree-l1"><a class="reference internal" href="course_contents/Tutorial.html">Nextflow fundamentals tutorial</a></li>
 </ul>
 <ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="resources.html">Resources</a></li>
diff --git a/course_contents/Contents.html b/course_contents/Contents.html
index ff2d699..0f55f80 100644
--- a/course_contents/Contents.html
+++ b/course_contents/Contents.html
@@ -49,7 +49,7 @@
     <link rel="author" title="About these documents" href="../about.html" />
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
-    <link rel="next" title="Resources" href="../resources.html" />
+    <link rel="next" title="Nextflow fundamentals tutorial" href="Tutorial.html" />
     <link rel="prev" title="Timing" href="../course_information/Timing.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
@@ -172,6 +172,7 @@
 <p aria-level="2" class="caption" role="heading"><span class="caption-text">Course contents</span></p>
 <ul class="current nav bd-sidenav">
 <li class="toctree-l1 current active"><a class="current reference internal" href="#">Contents</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Tutorial.html">Nextflow fundamentals tutorial</a></li>
 </ul>
 <ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="../resources.html">Resources</a></li>
@@ -359,11 +360,11 @@ <h1>Contents<a class="headerlink" href="#contents" title="Link to this heading">
       </div>
     </a>
     <a class="right-next"
-       href="../resources.html"
+       href="Tutorial.html"
        title="next page">
       <div class="prev-next-info">
         <p class="prev-next-subtitle">next</p>
-        <p class="prev-next-title">Resources</p>
+        <p class="prev-next-title">Nextflow fundamentals tutorial</p>
       </div>
       <i class="fa-solid fa-angle-right"></i>
     </a>
diff --git a/course_contents/Tutorial.html b/course_contents/Tutorial.html
new file mode 100644
index 0000000..56cc872
--- /dev/null
+++ b/course_contents/Tutorial.html
@@ -0,0 +1,436 @@
+
+<!DOCTYPE html>
+
+
+<html lang="en" data-content_root="../" >
+
+  <head>
+    <meta charset="utf-8" />
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
+
+    <title>Nextflow fundamentals tutorial &#8212; Nextflow training notes template  documentation</title>
+  
+  
+  
+  <script data-cfasync="false">
+    document.documentElement.dataset.mode = localStorage.getItem("mode") || "";
+    document.documentElement.dataset.theme = localStorage.getItem("theme") || "";
+  </script>
+  <!-- 
+    this give us a css class that will be invisible only if js is disabled 
+  -->
+  <noscript>
+    <style>
+      .pst-js-only { display: none !important; }
+
+    </style>
+  </noscript>
+  
+  <!-- Loaded before other Sphinx assets -->
+  <link href="../_static/styles/theme.css?digest=26a4bc78f4c0ddb94549" rel="stylesheet" />
+<link href="../_static/styles/pydata-sphinx-theme.css?digest=26a4bc78f4c0ddb94549" rel="stylesheet" />
+
+    <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=a746c00c" />
+    <link rel="stylesheet" type="text/css" href="../_static/styles/sphinx-book-theme.css?v=a3416100" />
+    <link rel="stylesheet" type="text/css" href="../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+  
+  <!-- So that users can add custom icons -->
+  <script src="../_static/scripts/fontawesome.js?digest=26a4bc78f4c0ddb94549"></script>
+  <!-- Pre-loaded scripts that we'll load fully later -->
+  <link rel="preload" as="script" href="../_static/scripts/bootstrap.js?digest=26a4bc78f4c0ddb94549" />
+<link rel="preload" as="script" href="../_static/scripts/pydata-sphinx-theme.js?digest=26a4bc78f4c0ddb94549" />
+
+    <script src="../_static/documentation_options.js?v=9eb32ce0"></script>
+    <script src="../_static/doctools.js?v=9bcbadda"></script>
+    <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+    <script src="../_static/scripts/sphinx-book-theme.js?v=887ef09a"></script>
+    <script>DOCUMENTATION_OPTIONS.pagename = 'course_contents/Tutorial';</script>
+    <script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
+    <link rel="author" title="About these documents" href="../about.html" />
+    <link rel="index" title="Index" href="../genindex.html" />
+    <link rel="search" title="Search" href="../search.html" />
+    <link rel="next" title="Resources" href="../resources.html" />
+    <link rel="prev" title="Contents" href="Contents.html" />
+  <meta name="viewport" content="width=device-width, initial-scale=1"/>
+  <meta name="docsearch:language" content="en"/>
+  <meta name="docsearch:version" content="" />
+  </head>
+  
+  
+  <body data-bs-spy="scroll" data-bs-target=".bd-toc-nav" data-offset="180" data-bs-root-margin="0px 0px -60%" data-default-mode="">
+
+  
+  
+  <div id="pst-skip-link" class="skip-link d-print-none"><a href="#main-content">Skip to main content</a></div>
+  
+  <div id="pst-scroll-pixel-helper"></div>
+  
+  <button type="button" class="btn rounded-pill" id="pst-back-to-top">
+    <i class="fa-solid fa-arrow-up"></i>Back to top</button>
+
+  
+  <dialog id="pst-search-dialog">
+    
+<form class="bd-search d-flex align-items-center"
+      action="../search.html"
+      method="get">
+  <i class="fa-solid fa-magnifying-glass"></i>
+  <input type="search"
+         class="form-control"
+         name="q"
+         placeholder="Search..."
+         aria-label="Search..."
+         autocomplete="off"
+         autocorrect="off"
+         autocapitalize="off"
+         spellcheck="false"/>
+  <span class="search-button__kbd-shortcut"><kbd class="kbd-shortcut__modifier">Ctrl</kbd>+<kbd>K</kbd></span>
+</form>
+  </dialog>
+
+  <div class="pst-async-banner-revealer d-none">
+  <aside id="bd-header-version-warning" class="d-none d-print-none" aria-label="Version warning"></aside>
+</div>
+
+  
+    <header class="bd-header navbar navbar-expand-lg bd-navbar d-print-none">
+    </header>
+  
+
+  <div class="bd-container">
+    <div class="bd-container__inner bd-page-width">
+      
+      
+      
+      <dialog id="pst-primary-sidebar-modal"></dialog>
+      <div id="pst-primary-sidebar" class="bd-sidebar-primary bd-sidebar">
+        
+
+  
+  <div class="sidebar-header-items sidebar-primary__section">
+    
+    
+    
+    
+  </div>
+  
+    <div class="sidebar-primary-items__start sidebar-primary__section">
+        <div class="sidebar-primary-item">
+
+  
+    
+  
+
+<a class="navbar-brand logo" href="../index.html">
+  
+  
+  
+  
+  
+  
+    <p class="title logo__title">Nextflow training notes template  documentation</p>
+  
+</a></div>
+        <div class="sidebar-primary-item"><ul class="navbar-icon-links"
+    aria-label="Icon Links">
+        <li class="nav-item">
+          
+          
+          
+          
+          
+          
+          
+          
+          <a href="https://github.com/enryh/" title="GitHub" class="nav-link pst-navbar-icon" rel="noopener" target="_blank" data-bs-toggle="tooltip" data-bs-placement="bottom"><i class="fa-brands fa-square-github fa-lg" aria-hidden="true"></i>
+            <span class="sr-only">GitHub</span></a>
+        </li>
+</ul></div>
+        <div class="sidebar-primary-item">
+
+<button class="btn search-button-field search-button__button pst-js-only" title="Search" aria-label="Search" data-bs-placement="bottom" data-bs-toggle="tooltip">
+ <i class="fa-solid fa-magnifying-glass"></i>
+ <span class="search-button__default-text">Search</span>
+ <span class="search-button__kbd-shortcut"><kbd class="kbd-shortcut__modifier">Ctrl</kbd>+<kbd class="kbd-shortcut__modifier">K</kbd></span>
+</button></div>
+        <div class="sidebar-primary-item"><nav class="bd-links bd-docs-nav" aria-label="Main">
+    <div class="bd-toc-item navbar-nav active">
+        <ul class="nav bd-sidenav">
+<li class="toctree-l1"><a class="reference internal" href="../about.html">About</a></li>
+
+</ul>
+<p aria-level="2" class="caption" role="heading"><span class="caption-text">A topic</span></p>
+<ul class="nav bd-sidenav">
+<li class="toctree-l1"><a class="reference internal" href="../folder_topic/article_topic.html">Headline of the article</a></li>
+</ul>
+<p aria-level="2" class="caption" role="heading"><span class="caption-text">Course information</span></p>
+<ul class="nav bd-sidenav">
+<li class="toctree-l1"><a class="reference internal" href="../course_information/Instructions.html">Instructions</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../course_information/Location.html">Location</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../course_information/Timing.html">Timing</a></li>
+</ul>
+<p aria-level="2" class="caption" role="heading"><span class="caption-text">Course contents</span></p>
+<ul class="current nav bd-sidenav">
+<li class="toctree-l1"><a class="reference internal" href="Contents.html">Contents</a></li>
+<li class="toctree-l1 current active"><a class="current reference internal" href="#">Nextflow fundamentals tutorial</a></li>
+</ul>
+<ul class="nav bd-sidenav">
+<li class="toctree-l1"><a class="reference internal" href="../resources.html">Resources</a></li>
+</ul>
+
+    </div>
+</nav></div>
+    </div>
+  
+  
+  <div class="sidebar-primary-items__end sidebar-primary__section">
+  </div>
+  
+  <div id="rtd-footer-container"></div>
+
+
+      </div>
+      
+      <main id="main-content" class="bd-main" role="main">
+        
+        
+
+<div class="sbt-scroll-pixel-helper"></div>
+
+          <div class="bd-content">
+            <div class="bd-article-container">
+              
+              <div class="bd-header-article d-print-none">
+<div class="header-article-items header-article__inner">
+  
+    <div class="header-article-items__start">
+      
+        <div class="header-article-item"><button class="sidebar-toggle primary-toggle btn btn-sm" title="Toggle primary sidebar" data-bs-placement="bottom" data-bs-toggle="tooltip">
+  <span class="fa-solid fa-bars"></span>
+</button></div>
+      
+    </div>
+  
+  
+    <div class="header-article-items__end">
+      
+        <div class="header-article-item">
+
+<div class="article-header-buttons">
+
+
+<a href="https://github.com/enryh/notes_template" target="_blank"
+   class="btn btn-sm btn-source-repository-button"
+   title="Source repository"
+   data-bs-placement="bottom" data-bs-toggle="tooltip"
+>
+  
+
+<span class="btn__icon-container">
+  <i class="fab fa-github"></i>
+  </span>
+
+</a>
+
+
+
+
+
+
+<div class="dropdown dropdown-download-buttons">
+  <button class="btn dropdown-toggle" type="button" data-bs-toggle="dropdown" aria-expanded="false" aria-label="Download this page">
+    <i class="fas fa-download"></i>
+  </button>
+  <ul class="dropdown-menu">
+      
+      
+      
+      <li><a href="../_sources/course_contents/Tutorial.md" target="_blank"
+   class="btn btn-sm btn-download-source-button dropdown-item"
+   title="Download source file"
+   data-bs-placement="left" data-bs-toggle="tooltip"
+>
+  
+
+<span class="btn__icon-container">
+  <i class="fas fa-file"></i>
+  </span>
+<span class="btn__text-container">.md</span>
+</a>
+</li>
+      
+      
+      
+      
+      <li>
+<button onclick="window.print()"
+  class="btn btn-sm btn-download-pdf-button dropdown-item"
+  title="Print to PDF"
+  data-bs-placement="left" data-bs-toggle="tooltip"
+>
+  
+
+<span class="btn__icon-container">
+  <i class="fas fa-file-pdf"></i>
+  </span>
+<span class="btn__text-container">.pdf</span>
+</button>
+</li>
+      
+  </ul>
+</div>
+
+
+
+
+<button onclick="toggleFullScreen()"
+  class="btn btn-sm btn-fullscreen-button"
+  title="Fullscreen mode"
+  data-bs-placement="bottom" data-bs-toggle="tooltip"
+>
+  
+
+<span class="btn__icon-container">
+  <i class="fas fa-expand"></i>
+  </span>
+
+</button>
+
+
+
+<button class="btn btn-sm nav-link pst-navbar-icon theme-switch-button pst-js-only" aria-label="Color mode" data-bs-title="Color mode"  data-bs-placement="bottom" data-bs-toggle="tooltip">
+  <i class="theme-switch fa-solid fa-sun                fa-lg" data-mode="light" title="Light"></i>
+  <i class="theme-switch fa-solid fa-moon               fa-lg" data-mode="dark"  title="Dark"></i>
+  <i class="theme-switch fa-solid fa-circle-half-stroke fa-lg" data-mode="auto"  title="System Settings"></i>
+</button>
+
+
+<button class="btn btn-sm pst-navbar-icon search-button search-button__button pst-js-only" title="Search" aria-label="Search" data-bs-placement="bottom" data-bs-toggle="tooltip">
+    <i class="fa-solid fa-magnifying-glass fa-lg"></i>
+</button>
+
+</div></div>
+      
+    </div>
+  
+</div>
+</div>
+              
+              
+
+<div id="jb-print-docs-body" class="onlyprint">
+    <h1>Nextflow fundamentals tutorial</h1>
+    <!-- Table of contents -->
+    <div id="print-main-content">
+        <div id="jb-print-toc">
+            
+        </div>
+    </div>
+</div>
+
+              
+                
+<div id="searchbox"></div>
+                <article class="bd-article">
+                  
+  <section class="tex2jax_ignore mathjax_ignore" id="nextflow-fundamentals-tutorial">
+<h1>Nextflow fundamentals tutorial<a class="headerlink" href="#nextflow-fundamentals-tutorial" title="Link to this heading">#</a></h1>
+<p>For DTU-Biosustain and DTU-Bioenginnering</p>
+<p>Print the current version, system and runtime:</p>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>:caption:<span class="w"> </span>Verify<span class="w"> </span>java<span class="w"> </span>installation:
+
+nextflow<span class="w"> </span>info
+</pre></div>
+</div>
+<p>Run hello.nf as it is, passing a parameter from the command line and after changing the code in the second process (rev $y) using –resume
+nextflow run hello.nf
+nextflow run hello.nf –greeting ‘Hello Albert’
+nextflow run hello.nf –greeting ‘Hello Albert’ -resume</p>
+</section>
+
+
+                </article>
+              
+
+              
+              
+              
+              
+                <footer class="prev-next-footer d-print-none">
+                  
+<div class="prev-next-area">
+    <a class="left-prev"
+       href="Contents.html"
+       title="previous page">
+      <i class="fa-solid fa-angle-left"></i>
+      <div class="prev-next-info">
+        <p class="prev-next-subtitle">previous</p>
+        <p class="prev-next-title">Contents</p>
+      </div>
+    </a>
+    <a class="right-next"
+       href="../resources.html"
+       title="next page">
+      <div class="prev-next-info">
+        <p class="prev-next-subtitle">next</p>
+        <p class="prev-next-title">Resources</p>
+      </div>
+      <i class="fa-solid fa-angle-right"></i>
+    </a>
+</div>
+                </footer>
+              
+            </div>
+            
+            
+              
+            
+          </div>
+          <footer class="bd-footer-content">
+            
+<div class="bd-footer-content__inner container">
+  
+  <div class="footer-item">
+    
+<p class="component-author">
+By Albert Palleja
+</p>
+
+  </div>
+  
+  <div class="footer-item">
+    
+
+  <p class="copyright">
+    
+      © Copyright 2024, DTU Biosustain, Informatics Platform, DSP.
+      <br/>
+    
+  </p>
+
+  </div>
+  
+  <div class="footer-item">
+    
+  </div>
+  
+  <div class="footer-item">
+    
+  </div>
+  
+</div>
+          </footer>
+        
+
+      </main>
+    </div>
+  </div>
+  
+  <!-- Scripts loaded after <body> so the DOM is not blocked -->
+  <script defer src="../_static/scripts/bootstrap.js?digest=26a4bc78f4c0ddb94549"></script>
+<script defer src="../_static/scripts/pydata-sphinx-theme.js?digest=26a4bc78f4c0ddb94549"></script>
+
+  <footer class="bd-footer">
+  </footer>
+  </body>
+</html>
\ No newline at end of file
diff --git a/course_information/Instructions.html b/course_information/Instructions.html
index 5ccf00d..79e7c76 100644
--- a/course_information/Instructions.html
+++ b/course_information/Instructions.html
@@ -172,6 +172,7 @@
 <p aria-level="2" class="caption" role="heading"><span class="caption-text">Course contents</span></p>
 <ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="../course_contents/Contents.html">Contents</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../course_contents/Tutorial.html">Nextflow fundamentals tutorial</a></li>
 </ul>
 <ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="../resources.html">Resources</a></li>
@@ -350,26 +351,30 @@ <h2>Opening the Nextflow environment<a class="headerlink" href="#opening-the-nex
 <p>Click on button <strong>Code</strong> and click on the Codespaces tab. There click on <strong>Create codespace</strong>. Now your Nextflow environment will be built following the instructions in devcontainer.json file (i.e. installing Ubuntu, Docker, VSCode with Docker extension) with additional customization added in the Dockerfile (i.e, installing java and Docker dependencies).</p>
 <p>To learn more about Github codespaces go <a class="reference external" href="https://github.com/features/codespaces" rel="noopener noreferrer" target="_blank">here</a></p>
 <p>Now, Nextflow should be ready to run in your GitHub Codespace environment! Let’s check that you have a fully functional environment.</p>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>:caption:<span class="w"> </span>Verify<span class="w"> </span>java<span class="w"> </span>installation:
-
-java<span class="w"> </span>-version
+<div class="literal-block-wrapper docutils container" id="id1">
+<div class="code-block-caption"><span class="caption-text">Verify java installation:</span><a class="headerlink" href="#id1" title="Link to this code">#</a></div>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>java<span class="w"> </span>-version
 </pre></div>
 </div>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>:caption:<span class="w"> </span>Verify<span class="w"> </span>Nextflow<span class="w"> </span>installation:
-
-nextflow<span class="w"> </span>-v
+</div>
+<div class="literal-block-wrapper docutils container" id="id2">
+<div class="code-block-caption"><span class="caption-text">Verify Nextflow installation:</span><a class="headerlink" href="#id2" title="Link to this code">#</a></div>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>nextflow<span class="w"> </span>-v
 </pre></div>
 </div>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>:caption:<span class="w"> </span>Nextflow<span class="w"> </span>information:
-
-nextflow<span class="w"> </span>info
+</div>
+<div class="literal-block-wrapper docutils container" id="id3">
+<div class="code-block-caption"><span class="caption-text">Nextflow information:</span><a class="headerlink" href="#id3" title="Link to this code">#</a></div>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>nextflow<span class="w"> </span>info
 </pre></div>
 </div>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>:caption:<span class="w"> </span>Verify<span class="w"> </span>Docker<span class="w"> </span>installation:
-
-docker<span class="w"> </span>--version
+</div>
+<div class="literal-block-wrapper docutils container" id="id4">
+<div class="code-block-caption"><span class="caption-text">Verify Docker installation:</span><a class="headerlink" href="#id4" title="Link to this code">#</a></div>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>docker<span class="w"> </span>--version
 </pre></div>
 </div>
+</div>
 </section>
 </section>
 
diff --git a/course_information/Location.html b/course_information/Location.html
index 87b8f9b..db804d1 100644
--- a/course_information/Location.html
+++ b/course_information/Location.html
@@ -172,6 +172,7 @@
 <p aria-level="2" class="caption" role="heading"><span class="caption-text">Course contents</span></p>
 <ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="../course_contents/Contents.html">Contents</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../course_contents/Tutorial.html">Nextflow fundamentals tutorial</a></li>
 </ul>
 <ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="../resources.html">Resources</a></li>
diff --git a/course_information/Timing.html b/course_information/Timing.html
index 81ac13d..35a69c2 100644
--- a/course_information/Timing.html
+++ b/course_information/Timing.html
@@ -172,6 +172,7 @@
 <p aria-level="2" class="caption" role="heading"><span class="caption-text">Course contents</span></p>
 <ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="../course_contents/Contents.html">Contents</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../course_contents/Tutorial.html">Nextflow fundamentals tutorial</a></li>
 </ul>
 <ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="../resources.html">Resources</a></li>
diff --git a/folder_topic/article_topic.html b/folder_topic/article_topic.html
index 05cb73d..3617e78 100644
--- a/folder_topic/article_topic.html
+++ b/folder_topic/article_topic.html
@@ -172,6 +172,7 @@
 <p aria-level="2" class="caption" role="heading"><span class="caption-text">Course contents</span></p>
 <ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="../course_contents/Contents.html">Contents</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../course_contents/Tutorial.html">Nextflow fundamentals tutorial</a></li>
 </ul>
 <ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="../resources.html">Resources</a></li>
diff --git a/genindex.html b/genindex.html
index 48863ed..95fad58 100644
--- a/genindex.html
+++ b/genindex.html
@@ -171,6 +171,7 @@
 <p aria-level="2" class="caption" role="heading"><span class="caption-text">Course contents</span></p>
 <ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="course_contents/Contents.html">Contents</a></li>
+<li class="toctree-l1"><a class="reference internal" href="course_contents/Tutorial.html">Nextflow fundamentals tutorial</a></li>
 </ul>
 <ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="resources.html">Resources</a></li>
diff --git a/index.html b/index.html
index e1313b4..6b27b22 100644
--- a/index.html
+++ b/index.html
@@ -173,6 +173,7 @@
 <p aria-level="2" class="caption" role="heading"><span class="caption-text">Course contents</span></p>
 <ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="course_contents/Contents.html">Contents</a></li>
+<li class="toctree-l1"><a class="reference internal" href="course_contents/Tutorial.html">Nextflow fundamentals tutorial</a></li>
 </ul>
 <ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="resources.html">Resources</a></li>
diff --git a/objects.inv b/objects.inv
index 9675242c0afcb7bab4ed517d1cdc9eff617395b4..9f28103c401727b7ec4ddcbf0fadc1293d227a93 100644
GIT binary patch
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diff --git a/resources.html b/resources.html
index 9630575..f6127e5 100644
--- a/resources.html
+++ b/resources.html
@@ -49,7 +49,7 @@
     <link rel="author" title="About these documents" href="about.html" />
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
-    <link rel="prev" title="Contents" href="course_contents/Contents.html" />
+    <link rel="prev" title="Nextflow fundamentals tutorial" href="course_contents/Tutorial.html" />
   <meta name="viewport" content="width=device-width, initial-scale=1"/>
   <meta name="docsearch:language" content="en"/>
   <meta name="docsearch:version" content="" />
@@ -171,6 +171,7 @@
 <p aria-level="2" class="caption" role="heading"><span class="caption-text">Course contents</span></p>
 <ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="course_contents/Contents.html">Contents</a></li>
+<li class="toctree-l1"><a class="reference internal" href="course_contents/Tutorial.html">Nextflow fundamentals tutorial</a></li>
 </ul>
 <ul class="current nav bd-sidenav">
 <li class="toctree-l1 current active"><a class="current reference internal" href="#">Resources</a></li>
@@ -379,12 +380,12 @@ <h2>Citations<a class="headerlink" href="#citations" title="Link to this heading
                   
 <div class="prev-next-area">
     <a class="left-prev"
-       href="course_contents/Contents.html"
+       href="course_contents/Tutorial.html"
        title="previous page">
       <i class="fa-solid fa-angle-left"></i>
       <div class="prev-next-info">
         <p class="prev-next-subtitle">previous</p>
-        <p class="prev-next-title">Contents</p>
+        <p class="prev-next-title">Nextflow fundamentals tutorial</p>
       </div>
     </a>
 </div>
diff --git a/search.html b/search.html
index dd3987d..b83e747 100644
--- a/search.html
+++ b/search.html
@@ -173,6 +173,7 @@
 <p aria-level="2" class="caption" role="heading"><span class="caption-text">Course contents</span></p>
 <ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="course_contents/Contents.html">Contents</a></li>
+<li class="toctree-l1"><a class="reference internal" href="course_contents/Tutorial.html">Nextflow fundamentals tutorial</a></li>
 </ul>
 <ul class="nav bd-sidenav">
 <li class="toctree-l1"><a class="reference internal" href="resources.html">Resources</a></li>
diff --git a/searchindex.js b/searchindex.js
index 250a7da..07b1ddf 100644
--- a/searchindex.js
+++ b/searchindex.js
@@ -1 +1 @@
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