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@apalleja
apalleja committed Nov 25, 2024
1 parent 88916b6 commit 0f70f3e
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10 changes: 5 additions & 5 deletions _sources/course_contents/Tutorial.md
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Expand Up @@ -149,7 +149,7 @@ process sayHello {
Changing the code to write the variable (containing our grreting) in the output file:

```bash
echo '$greeting' > output.txt
echo "$greeting" > output.txt
```
### 3. Creating an input channel

Expand Down Expand Up @@ -318,7 +318,7 @@ process sayHello {
script:
"""
echo '$greeting' > '${greeting}-output.txt'
echo "$greeting" > "${greeting}-output.txt"
"""
}
```
Expand All @@ -345,7 +345,7 @@ Finally last modification to our script. Usually workflows start from a sample f
```bash
mkdir data
cd data
echo "Hello,Bonjour,Hola,Hej," > greetings.csv
echo "Hello,Bonjour,Hola,Hej" > greetings.csv
less greetings.csv
cd ..
```
Expand Down Expand Up @@ -416,7 +416,7 @@ process sayHello {
script:
"""
echo '$greeting' > '$greeting-output.txt'
echo "$greeting" > "$greeting-output.txt"
"""
}
Expand All @@ -437,7 +437,7 @@ process convertToUpper {
// now we add the bash code to convert the greeting to uppercase
script:
"""
cat '$input_file' | tr '[a-z]' '[A-Z]' > UPPER-${input_file}
cat "$input_file" | tr '[a-z]' '[A-Z]' > UPPER-${input_file}
"""
}
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10 changes: 5 additions & 5 deletions course_contents/Tutorial.html
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Expand Up @@ -496,7 +496,7 @@ <h3>1. Input definition to the process block:<a class="headerlink" href="#input-
<section id="editing-the-process-command-to-use-the-input-variable">
<h3>2. Editing the process command to use the input variable<a class="headerlink" href="#editing-the-process-command-to-use-the-input-variable" title="Link to this heading">#</a></h3>
<p>Changing the code to write the variable (containing our grreting) in the output file:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">echo</span><span class="w"> </span><span class="s1">&#39;$greeting&#39;</span><span class="w"> </span>&gt;<span class="w"> </span>output.txt
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">echo</span><span class="w"> </span><span class="s2">&quot;</span><span class="nv">$greeting</span><span class="s2">&quot;</span><span class="w"> </span>&gt;<span class="w"> </span>output.txt
</pre></div>
</div>
</section>
Expand Down Expand Up @@ -665,7 +665,7 @@ <h2>Let’s run the script on a batch of input values<a class="headerlink" href=

<span class="w"> </span><span class="nl">script:</span>
<span class="w"> </span><span class="s2">&quot;&quot;&quot;</span>
<span class="s2"> echo &#39;$greeting&#39; &gt; &#39;${greeting}-output.txt&#39;</span>
<span class="s2"> echo &quot;$greeting&quot; &gt; &quot;${greeting}-output.txt&quot;</span>
<span class="s2"> &quot;&quot;&quot;</span>
<span class="o">}</span>
</pre></div>
Expand All @@ -688,7 +688,7 @@ <h2>Take a file source of input values (a sample file)<a class="headerlink" href
<p>Finally last modification to our script. Usually workflows start from a sample file. In Nextflow and in nf-core standards this is usually called <code class="docutils literal notranslate"><span class="pre">samplesheet.csv</span></code>. We will create a file called <code class="docutils literal notranslate"><span class="pre">greetings.csv</span></code> for our example pipeline and save it in a folder called <code class="docutils literal notranslate"><span class="pre">data</span></code>.</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>mkdir<span class="w"> </span>data
<span class="nb">cd</span><span class="w"> </span>data
<span class="nb">echo</span><span class="w"> </span><span class="s2">&quot;Hello,Bonjour,Hola,Hej,&quot;</span><span class="w"> </span>&gt;<span class="w"> </span>greetings.csv
<span class="nb">echo</span><span class="w"> </span><span class="s2">&quot;Hello,Bonjour,Hola,Hej&quot;</span><span class="w"> </span>&gt;<span class="w"> </span>greetings.csv
less<span class="w"> </span>greetings.csv
<span class="nb">cd</span><span class="w"> </span>..<span class="w"> </span>
</pre></div>
Expand Down Expand Up @@ -755,7 +755,7 @@ <h2>Full script<a class="headerlink" href="#full-script" title="Link to this hea

<span class="w"> </span><span class="nl">script:</span>
<span class="w"> </span><span class="s2">&quot;&quot;&quot;</span>
<span class="s2"> echo &#39;$greeting&#39; &gt; &#39;$greeting-output.txt&#39;</span>
<span class="s2"> echo &quot;$greeting&quot; &gt; &quot;$greeting-output.txt&quot;</span>
<span class="s2"> &quot;&quot;&quot;</span>
<span class="o">}</span>

Expand All @@ -776,7 +776,7 @@ <h2>Full script<a class="headerlink" href="#full-script" title="Link to this hea
<span class="w"> </span><span class="c1">// now we add the bash code to convert the greeting to uppercase</span>
<span class="w"> </span><span class="nl">script:</span>
<span class="w"> </span><span class="s2">&quot;&quot;&quot;</span>
<span class="s2"> cat &#39;$input_file&#39; | tr &#39;[a-z]&#39; &#39;[A-Z]&#39; &gt; UPPER-${input_file}</span>
<span class="s2"> cat &quot;$input_file&quot; | tr &#39;[a-z]&#39; &#39;[A-Z]&#39; &gt; UPPER-${input_file}</span>
<span class="s2"> &quot;&quot;&quot;</span>
<span class="o">}</span>

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