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biosustain · Nov 8, 2024 · 09c42fe · 09c42fe
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diff --git a/.doctrees/course_contents/Tutorial.doctree b/.doctrees/course_contents/Tutorial.doctree
diff --git a/.doctrees/environment.pickle b/.doctrees/environment.pickle
diff --git a/_sources/course_contents/Tutorial.md b/_sources/course_contents/Tutorial.md
@@ -12,7 +12,7 @@ nextflow info
 
 Let's run our first script, 'Hello World!' script.
 
-```
+```{code-block} groovy
 :caption: hello.nf
 
 #!/usr/bin/env nextflow

diff --git a/course_contents/Tutorial.html b/course_contents/Tutorial.html
@@ -364,35 +364,36 @@ <h2>First enviroment verifications<a class="headerlink" href="#first-enviroment-
 <section id="running-our-first-script">
 <h2>Running our first script<a class="headerlink" href="#running-our-first-script" title="Link to this heading">#</a></h2>
 <p>Let’s run our first script, ‘Hello World!’ script.</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="p">:</span><span class="n">caption</span><span class="p">:</span> <span class="n">hello</span><span class="o">.</span><span class="n">nf</span>
-
-<span class="c1">#!/usr/bin/env nextflow</span>
-
-<span class="o">/*</span>
- <span class="o">*</span> <span class="n">Use</span> <span class="n">echo</span> <span class="n">to</span> <span class="nb">print</span> <span class="s1">&#39;Hello World!&#39;</span> <span class="n">to</span> <span class="n">standard</span> <span class="n">out</span>
- <span class="o">*/</span>
-<span class="o">//</span> <span class="n">A</span> <span class="n">process</span>
-<span class="n">process</span> <span class="n">sayHello</span> <span class="p">{</span>
-
-    <span class="o">//</span><span class="n">directives</span>
-    <span class="n">output</span><span class="p">:</span>
-        <span class="n">stdout</span>
-    
-    <span class="o">//</span> <span class="n">code</span> <span class="n">block</span> <span class="p">(</span><span class="n">here</span> <span class="n">using</span> <span class="n">bash</span><span class="p">)</span>
-    <span class="n">script</span><span class="p">:</span> 
-<span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
-<span class="sd">    echo &#39;Hello World!&#39;</span>
-<span class="sd">    &quot;&quot;&quot;</span>
-<span class="p">}</span>
-
-<span class="o">//</span> <span class="n">the</span> <span class="n">workflow</span>
-<span class="n">workflow</span> <span class="p">{</span>
-
-    <span class="o">//</span> <span class="n">emit</span> <span class="n">a</span> <span class="n">greeting</span>
-    <span class="n">sayHello</span><span class="p">()</span>
-<span class="p">}</span>
+<div class="literal-block-wrapper docutils container" id="id1">
+<div class="code-block-caption"><span class="caption-text">hello.nf</span><a class="headerlink" href="#id1" title="Link to this code">#</a></div>
+<div class="highlight-groovy notranslate"><div class="highlight"><pre><span></span><span class="cp">#!/usr/bin/env nextflow</span>
+
+<span class="cm">/*</span>
+<span class="cm"> * Use echo to print &#39;Hello World!&#39; to standard out</span>
+<span class="cm"> */</span>
+<span class="c1">// A process</span>
+<span class="n">process</span><span class="w"> </span><span class="n">sayHello</span><span class="w"> </span><span class="o">{</span>
+
+<span class="w">    </span><span class="c1">//directives</span>
+<span class="w">    </span><span class="nl">output:</span>
+<span class="w">        </span><span class="n">stdout</span>
+<span class="w">    </span>
+<span class="w">    </span><span class="c1">// code block (here using bash)</span>
+<span class="w">    </span><span class="nl">script:</span><span class="w"> </span>
+<span class="w">    </span><span class="s2">&quot;&quot;&quot;</span>
+<span class="s2">    echo &#39;Hello World!&#39;</span>
+<span class="s2">    &quot;&quot;&quot;</span>
+<span class="o">}</span>
+
+<span class="c1">// the workflow</span>
+<span class="n">workflow</span><span class="w"> </span><span class="o">{</span>
+
+<span class="w">    </span><span class="c1">// emit a greeting</span>
+<span class="w">    </span><span class="n">sayHello</span><span class="o">()</span>
+<span class="o">}</span>
 </pre></div>
 </div>
+</div>
 <p>As you can see, a Nextflow script involves two main types of core components: process/es and the workflow. Each process describes what operation(s) should be performed (print ‘Hello World!’), while the workflow describes the dataflow logic that connects the various steps.</p>
 <p>Let’s try to run this code in your codespace:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="p">:</span><span class="n">caption</span><span class="p">:</span> <span class="n">Running</span> <span class="n">hello</span><span class="o">-</span><span class="n">world</span><span class="o">.</span><span class="n">nf</span>