deploy: 02fb95d

_sources/course_contents/RunningRealWorkflow.md

@@ -15,7 +15,7 @@ To be able to run this pipeline we will clone the training repository from Nextf
 
 First cloning with `git clone`:
 ```bash
-git clone https://github.com/nextflow-io/training.git
+git clone https://github.com/nextflow-io/training.git --depth 1
 ```
 And then move to `training/nf-training`:
 ```bash
@@ -58,4 +58,4 @@ Let's run again the workflow by calling our config file:
 sudo nextflow run script7.nf -c course.config
 ```
 
- You are are welcome to have a look to the file that was downloaded `nextflow.config`, to see what usually these files contain and realise how important they are to setup the environment for the nextflow runs. The config file `nextflow.config` must be in the same folder where you are running your main script (`main.nf`) otherwise you need to specify the location with `-c`
+You are are welcome to have a look to the file that was downloaded `nextflow.config`, to see what usually these files contain and realise how important they are to setup the environment for the nextflow runs. The config file `nextflow.config` must be in the same folder where you are running your main script (`main.nf`) otherwise you need to specify the location with `-c`

_sources/course_contents/Tutorial.md

@@ -281,19 +281,16 @@ Workflows typically run on batches of inputs that are meant to be processed in b
 
 There are different factory channels to create the channels. Here you have an example where I used factory `Channel.fromFilePairs()` fastq read files.
 
-> params.reads = "$projectDir/data/*_{1,2}.fq.gz"
->
-> Channel
-
->        .fromFilePairs(params.reads, checkIfExists: true)
-
->        .toSortedList( { a, b -> a[0] <=> b[0] } )
-
->        .flatMap()
-
->        .set { read_pairs_ch }
-
->        read_pairs_ch.view()
+```groovy
+params.reads = "$projectDir/data/*_{1,2}.fq.gz"
+
+Channel
+    .fromFilePairs(params.reads, checkIfExists: true)
+    .toSortedList( { a, b -> a[0] <=> b[0] } )
+    .flatMap()
+    .set { read_pairs_ch }
+    read_pairs_ch.view()
+```
 
 `.toSortedList`, `.flatMap`, `.set`, `.view` are operators to transform the channel and achieve the input files in the desired format.
 

course_contents/RunningRealWorkflow.html

@@ -343,7 +343,7 @@ <h1>RNA-Seq workflow<a class="headerlink" href="#rna-seq-workflow" title="Link t
 <p>This is based on this part of <a class="reference external" href="https://training.nextflow.io/basic_training/rnaseq_pipeline/" rel="noopener noreferrer" target="_blank">Nextflow tutorial</a>. There you can find the pipeline broken into the different pieces in a collection of 7 different scripts if you want to get into the details.</p>
 <p>To be able to run this pipeline we will clone the training repository from Nextflow training materials in github. Here you can enjoy the hello training, their fundamentals training based on the rnaseq pipeline and the advanced training with all data, files and scripts needed.</p>
 <p>First cloning with <code class="docutils literal notranslate"><span class="pre">git</span> <span class="pre">clone</span></code>:</p>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>git<span class="w"> </span>clone<span class="w"> </span>https://github.com/nextflow-io/training.git
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>git<span class="w"> </span>clone<span class="w"> </span>https://github.com/nextflow-io/training.git<span class="w"> </span>--depth<span class="w"> </span><span class="m">1</span>
 </pre></div>
 </div>
 <p>And then move to <code class="docutils literal notranslate"><span class="pre">training/nf-training</span></code>:</p>

course_contents/Tutorial.html

@@ -617,35 +617,16 @@ <h2>Let’s run the script on a batch of input values<a class="headerlink" href=
 <p>Workflows typically run on batches of inputs that are meant to be processed in bulk, so we want to upgrade the workflow to accept multiple input values.</p>
 <p><code class="docutils literal notranslate"><span class="pre">Channel.of()</span></code> factory we’ve been using is quite happy to accept more than one value. Imagine that these could be used to pass a list of genes, genomes or files …</p>
 <p>There are different factory channels to create the channels. Here you have an example where I used factory <code class="docutils literal notranslate"><span class="pre">Channel.fromFilePairs()</span></code> fastq read files.</p>
-<blockquote>
-<div><p>params.reads = “$projectDir/data/*_{1,2}.fq.gz”</p>
-<p>Channel</p>
-</div></blockquote>
-<blockquote>
-<div><div class="highlight-none notranslate"><div class="highlight"><pre><span></span>   .fromFilePairs(params.reads, checkIfExists: true)
-</pre></div>
-</div>
-</div></blockquote>
-<blockquote>
-<div><div class="highlight-none notranslate"><div class="highlight"><pre><span></span>   .toSortedList( { a, b -&gt; a[0] &lt;=&gt; b[0] } )
-</pre></div>
-</div>
-</div></blockquote>
-<blockquote>
-<div><div class="highlight-none notranslate"><div class="highlight"><pre><span></span>   .flatMap()
-</pre></div>
-</div>
-</div></blockquote>
-<blockquote>
-<div><div class="highlight-none notranslate"><div class="highlight"><pre><span></span>   .set { read_pairs_ch }
-</pre></div>
-</div>
-</div></blockquote>
-<blockquote>
-<div><div class="highlight-none notranslate"><div class="highlight"><pre><span></span>   read_pairs_ch.view()
+<div class="highlight-groovy notranslate"><div class="highlight"><pre><span></span><span class="n">params</span><span class="o">.</span><span class="na">reads</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="s2">&quot;$projectDir/data/*_{1,2}.fq.gz&quot;</span>
+
+<span class="n">Channel</span>
+<span class="w">    </span><span class="o">.</span><span class="na">fromFilePairs</span><span class="o">(</span><span class="n">params</span><span class="o">.</span><span class="na">reads</span><span class="o">,</span><span class="w"> </span><span class="nl">checkIfExists:</span><span class="w"> </span><span class="kc">true</span><span class="o">)</span>
+<span class="w">    </span><span class="o">.</span><span class="na">toSortedList</span><span class="o">(</span><span class="w"> </span><span class="o">{</span><span class="w"> </span><span class="n">a</span><span class="o">,</span><span class="w"> </span><span class="n">b</span><span class="w"> </span><span class="o">-&gt;</span><span class="w"> </span><span class="n">a</span><span class="o">[</span><span class="mi">0</span><span class="o">]</span><span class="w"> </span><span class="o">&lt;=&gt;</span><span class="w"> </span><span class="n">b</span><span class="o">[</span><span class="mi">0</span><span class="o">]</span><span class="w"> </span><span class="o">}</span><span class="w"> </span><span class="o">)</span>
+<span class="w">    </span><span class="o">.</span><span class="na">flatMap</span><span class="o">()</span>
+<span class="w">    </span><span class="o">.</span><span class="na">set</span><span class="w"> </span><span class="o">{</span><span class="w"> </span><span class="n">read_pairs_ch</span><span class="w"> </span><span class="o">}</span>
+<span class="w">    </span><span class="n">read_pairs_ch</span><span class="o">.</span><span class="na">view</span><span class="o">()</span>
 </pre></div>
 </div>
-</div></blockquote>
 <p><code class="docutils literal notranslate"><span class="pre">.toSortedList</span></code>, <code class="docutils literal notranslate"><span class="pre">.flatMap</span></code>, <code class="docutils literal notranslate"><span class="pre">.set</span></code>, <code class="docutils literal notranslate"><span class="pre">.view</span></code> are operators to transform the channel and achieve the input files in the desired format.</p>
 <p>Back into our channel. Please modify the following, where do you need to add that?</p>
 <div class="highlight-groovy notranslate"><div class="highlight"><pre><span></span><span class="c1">// create a channel for inputs</span>