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-9e9c49e2
+338f3e2a

sessions/2_nf_dev_intro.html

@@ -223,7 +223,7 @@ <h3 class="anchored" data-anchor-id="learning-objectives">Learning Objectives:</
 </section>
 <section id="set-up-requirements" class="level3">
 <h3 class="anchored" data-anchor-id="set-up-requirements">Set up requirements</h3>
-<p>Please complete the <a href="./workshops/00_setup.html">Setup Instructions</a> before the course.</p>
+<p>Please complete the <a href="../workshops/00_setup.html">Setup Instructions</a> before the course.</p>
 <p>If you have any trouble, please get in contact with us ASAP via Slack/Teams.</p>
 </section>
 <section id="workshop-schedule" class="level3">
@@ -238,7 +238,7 @@ <h3 class="anchored" data-anchor-id="workshop-schedule">Workshop schedule</h3>
 </thead>
 <tbody>
 <tr class="odd">
-<td><a href="./workshops/00_setup.html">Setup</a></td>
+<td><a href="../workshops/00_setup.html">Setup</a></td>
 <td>Follow these instructions to install VS Code and setup your workspace</td>
 <td>Prior to workshop</td>
 </tr>

sitemap.xml

@@ -2,42 +2,46 @@
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-    <lastmod>2024-05-29T01:04:34.157Z</lastmod>
+    <lastmod>2024-05-29T01:20:43.219Z</lastmod>
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     <loc>https://PMCC-BioinformaticsCore.github.io/nextflow-intro-workshop/index.html</loc>
-    <lastmod>2024-05-29T01:04:33.255Z</lastmod>
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   <url>
     <loc>https://PMCC-BioinformaticsCore.github.io/nextflow-intro-workshop/workshops/2.3_tips_and_tricks.html</loc>
-    <lastmod>2024-05-29T01:04:31.453Z</lastmod>
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     <loc>https://PMCC-BioinformaticsCore.github.io/nextflow-intro-workshop/workshops/1.2_intro_nf_core.html</loc>
-    <lastmod>2024-05-29T01:04:30.469Z</lastmod>
+    <lastmod>2024-05-29T01:20:39.398Z</lastmod>
   </url>
   <url>
-    <loc>https://PMCC-BioinformaticsCore.github.io/nextflow-intro-workshop/workshops/1.1_intro_nextflow.html</loc>
-    <lastmod>2024-05-29T01:04:28.781Z</lastmod>
+    <loc>https://PMCC-BioinformaticsCore.github.io/nextflow-intro-workshop/workshops/4.1_draft_future_sess.html</loc>
+    <lastmod>2024-05-29T01:20:37.648Z</lastmod>
   </url>
   <url>
     <loc>https://PMCC-BioinformaticsCore.github.io/nextflow-intro-workshop/workshops/3.1_creating_a_workflow.html</loc>
-    <lastmod>2024-05-29T01:04:28.073Z</lastmod>
+    <lastmod>2024-05-29T01:20:36.497Z</lastmod>
+  </url>
+  <url>
+    <loc>https://PMCC-BioinformaticsCore.github.io/nextflow-intro-workshop/workshops/1.1_intro_nextflow.html</loc>
+    <lastmod>2024-05-29T01:20:37.202Z</lastmod>
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   <url>
     <loc>https://PMCC-BioinformaticsCore.github.io/nextflow-intro-workshop/workshops/2.2_troubleshooting.html</loc>
-    <lastmod>2024-05-29T01:04:29.577Z</lastmod>
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-    <lastmod>2024-05-29T01:04:30.910Z</lastmod>
+    <lastmod>2024-05-29T01:20:39.844Z</lastmod>
   </url>
   <url>
     <loc>https://PMCC-BioinformaticsCore.github.io/nextflow-intro-workshop/workshops/2.1_customise_and_run.html</loc>
-    <lastmod>2024-05-29T01:04:32.863Z</lastmod>
+    <lastmod>2024-05-29T01:20:41.860Z</lastmod>
   </url>
   <url>
     <loc>https://PMCC-BioinformaticsCore.github.io/nextflow-intro-workshop/sessions/1_intro_run_nf.html</loc>
-    <lastmod>2024-05-29T01:04:33.703Z</lastmod>
+    <lastmod>2024-05-29T01:20:42.751Z</lastmod>
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workshops/3.1_creating_a_workflow.html

@@ -826,7 +826,7 @@ <h3 class="anchored" data-anchor-id="perform-expression-quantification"><strong>
 <h3 class="anchored" data-anchor-id="quality-control"><strong>4.1.5. Quality Control</strong></h3>
 <p>Now, let’s implement a <code>FASTQC</code> quality control process for the input fastq reads.</p>
 <p><strong>Challenge:</strong></p>
-<p>Create a process called <code>FASTQC</code> that takes <code>reads_ch</code> as an input, and declares the process input to be a tuple matching the structure of <code>reads_ch</code>, where the first element is assigned the variable <code>sample_id</code>, and the second variable is assigned the varible <code>reads</code>. This <code>FASTQC</code> process will first create an output directory <code>fastqc_${sample_id}_logs</code>, then perform <code>fastqc</code> on the input <code>reads</code> and save the results in the newly created directory <code>fastqc_${sample_id}_logs</code>:</p>
+<p>Create a process called <code>FASTQC</code> that takes <code>reads_ch</code> as an input, and declares the process input to be a tuple matching the structure of <code>reads_ch</code>, where the first element is assigned the variable <code>sample_id</code>, and the second variable is assigned the variable <code>reads</code>. This <code>FASTQC</code> process will first create an output directory <code>fastqc_${sample_id}_logs</code>, then perform <code>fastqc</code> on the input <code>reads</code> and save the results in the newly created directory <code>fastqc_${sample_id}_logs</code>:</p>
 <div class="sourceCode" id="cb49"><pre class="sourceCode default code-with-copy"><code class="sourceCode default"><span id="cb49-1"><a href="#cb49-1" aria-hidden="true" tabindex="-1"></a>mkdir fastqc_${sample_id}_logs</span>
 <span id="cb49-2"><a href="#cb49-2" aria-hidden="true" tabindex="-1"></a>fastqc -o fastqc_${sample_id}_logs -f fastq -q ${reads}</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <p>Take <code>fastqc_${sample_id}_logs</code> as the output of the process, and assign it to the channel <code>fastqc_ch</code>. Finally, specify the process container to be the following:</p>
@@ -922,6 +922,7 @@ <h3 class="anchored" data-anchor-id="multiqc-report"><strong>4.1.6. MultiQC Repo
 </div>
 <hr>
 <p><sup><em>This workshop is adapted from <a href="https://training.nextflow.io/basic_training/">Fundamentals Training</a>, <a href="https://training.nextflow.io/advanced/">Advanced Training</a>, <a href="https://nf-co.re/docs/contributing/tutorials/creating_with_nf_core#creating-a-pipeline">Developer Tutorials</a>, and <a href="https://nextflow-io.github.io/patterns/">Nextflow Patterns</a> materials from Nextflow and nf-core</em></sup></p>
+<p><span style="font-size:0.5em;">^*<a href="./4.1_draft_future_sess.html">Draft for Future Sessions</a></span></p>
 
 
 </section>