Deployed d0014cf to 2024.9 with MkDocs 1.6.0 and mike 2.1.3

2024.9/course_schedule/index.html

@@ -812,7 +812,7 @@ <h2 id="day-1">Day 1</h2>
 <td>block 1</td>
 <td>9:00 AM</td>
 <td>10:30 AM</td>
-<td><a href="../day1/introduction">Introduction</a></td>
+<td><a href="../day1/introduction/">Introduction</a></td>
 </tr>
 <tr>
 <td></td>
@@ -824,7 +824,7 @@ <h2 id="day-1">Day 1</h2>
 <td>block 2</td>
 <td>11:00 AM</td>
 <td>12:30 PM</td>
-<td><a href="../day1/server_login">Setup</a> &amp; <a href="../day1/reproducibility">Reproducibility</a></td>
+<td><a href="../day1/server_login/">Setup</a> &amp; <a href="../day1/reproducibility/">Reproducibility</a></td>
 </tr>
 <tr>
 <td></td>
@@ -836,7 +836,7 @@ <h2 id="day-1">Day 1</h2>
 <td>block 3</td>
 <td>1:30 PM</td>
 <td>3:00 PM</td>
-<td><a href="../day1/alignment">Read alignment - basics</a></td>
+<td><a href="../day1/alignment/">Read alignment - basics</a></td>
 </tr>
 <tr>
 <td></td>
@@ -848,7 +848,7 @@ <h2 id="day-1">Day 1</h2>
 <td>block 4</td>
 <td>3:30 PM</td>
 <td>5:00 PM</td>
-<td><a href="../day1/alignment_advanced">Read alignment - advanced</a></td>
+<td><a href="../day1/alignment_advanced/">Read alignment - advanced</a></td>
 </tr>
 </tbody>
 </table>
@@ -867,7 +867,7 @@ <h2 id="day-2">Day 2</h2>
 <td>block 1</td>
 <td>9:00 AM</td>
 <td>10:30 AM</td>
-<td><a href="../day2/variant_calling_preparation">Variant calling - preparation</a></td>
+<td><a href="../day2/variant_calling_preparation/">Variant calling - preparation</a></td>
 </tr>
 <tr>
 <td></td>
@@ -879,7 +879,7 @@ <h2 id="day-2">Day 2</h2>
 <td>block 2</td>
 <td>11:00 AM</td>
 <td>12:30 PM</td>
-<td><a href="../day2/variant_calling">Variant calling</a></td>
+<td><a href="../day2/variant_calling/">Variant calling</a></td>
 </tr>
 <tr>
 <td></td>
@@ -891,7 +891,7 @@ <h2 id="day-2">Day 2</h2>
 <td>block 3</td>
 <td>1:30 PM</td>
 <td>3:00 PM</td>
-<td><a href="../day2/filtering_evaluation">Filtering &amp; evaluation</a> &amp; <a href="../day2/visualisation">Visualisation</a></td>
+<td><a href="../day2/filtering_evaluation/">Filtering &amp; evaluation</a> &amp; <a href="../day2/visualisation/">Visualisation</a></td>
 </tr>
 <tr>
 <td></td>
@@ -903,7 +903,7 @@ <h2 id="day-2">Day 2</h2>
 <td>block 4</td>
 <td>3:30 PM</td>
 <td>5:00 PM</td>
-<td><a href="../day2/annotation">Annotation</a></td>
+<td><a href="../day2/annotation/">Annotation</a></td>
 </tr>
 </tbody>
 </table>

2024.9/day1/alignment_advanced/index.html

@@ -1148,7 +1148,7 @@ <h3 id="5-apply-it-on-all-three-samples-with-pipes-and-loops">5. Apply it on all
 son lib3    H0164.6.ALXX140820  H0164.6
 </code></pre></div>
 </details>
-<p><strong>Exercise</strong> Generate a script called <code>C02_add_readgroups.sh</code> (in <code>~/project/scripts/C-all_samples</code>) to loop over the tab-delimited file (have a look at the last exercise in <a href="../server_login#loops">Setup</a>), and add the correct readgroups to the bam file of each sample with <code>gatk AddOrReplaceReadGroups</code>. </p>
+<p><strong>Exercise</strong> Generate a script called <code>C02_add_readgroups.sh</code> (in <code>~/project/scripts/C-all_samples</code>) to loop over the tab-delimited file (have a look at the last exercise in <a href="../server_login/#loops">Setup</a>), and add the correct readgroups to the bam file of each sample with <code>gatk AddOrReplaceReadGroups</code>. </p>
 <details class="hint">
 <summary>Hint</summary>
 <p>Try to just print the variables from a loop in order to check to see whether the loop performs according to your expectation. E.g.:</p>