From 1a18dc7245eea534d38ded52374b3eb3cc8eeb5c Mon Sep 17 00:00:00 2001
From: GitHub Actions <actions@github.com>
Date: Fri, 14 Jun 2024 19:03:15 +0000
Subject: [PATCH] site deploy

Auto-generated via {sandpaper}
Source  : 51a83a2f2da7236cb5f4166d1d468c8209df6121
Branch  : md-outputs
Author  : GitHub Actions <actions@github.com>
Time    : 2024-06-14 19:03:01 +0000
Message : markdown source builds

Auto-generated via {sandpaper}
Source  : 6b09fe5f293f57b4898f43106af706a57b5e3d59
Branch  : main
Author  : Erin Becker <erinstellabecker@gmail.com>
Time    : 2024-06-14 19:01:51 +0000
Message : Merge pull request #252 from Hanson19/patch-1

Step 3: Filter and report the incorrect directory in hightlight section
---
 02-quality-control.html            |  8 ++++----
 04-variant_calling.html            | 12 ++++++------
 05-automation.html                 |  2 +-
 aio.html                           | 20 ++++++++++----------
 instructor/02-quality-control.html |  8 ++++----
 instructor/04-variant_calling.html | 12 ++++++------
 instructor/05-automation.html      |  2 +-
 instructor/aio.html                | 20 ++++++++++----------
 md5sum.txt                         |  2 +-
 pkgdown.yml                        |  2 +-
 10 files changed, 44 insertions(+), 44 deletions(-)

diff --git a/02-quality-control.html b/02-quality-control.html
index a1b5b372..cbf4a099 100644
--- a/02-quality-control.html
+++ b/02-quality-control.html
@@ -489,7 +489,7 @@ <h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#e
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb9">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -705,7 +705,7 @@ <h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#e
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2">Show me the solution</h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb14">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -908,7 +908,7 @@ <h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#e
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <p>All of the reads contain usable data, but the quality decreases
 toward the end of the reads.</p>
@@ -1176,7 +1176,7 @@ <h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#e
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4">Show me the solution</h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
 <div class="accordion-body">
 <p>We can get the list of all failed tests using <code>grep</code>.</p>
 <div class="codewrapper sourceCode" id="cb42">
diff --git a/04-variant_calling.html b/04-variant_calling.html
index 77fc984f..40de4b4f 100644
--- a/04-variant_calling.html
+++ b/04-variant_calling.html
@@ -257,7 +257,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Variant Calling Workflow</h1>
-        <p>Last updated on 2023-05-04 |
+        <p>Last updated on 2024-06-14 |
         
         <a href="https://github.com/datacarpentry/wrangling-genomics/edit/main/episodes/04-variant_calling.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -347,7 +347,7 @@ <h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#e
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb2">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -616,7 +616,7 @@ <h3 class="callout-title">Filtering<a class="anchor" aria-label="anchor" href="#
 <div class="codewrapper sourceCode" id="cb20">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb20-1"><a href="#cb20-1" tabindex="-1"></a><span class="ex">$</span> bcftools stats results/bcf/SRR2584866_variants.vcf <span class="kw">|</span> <span class="fu">grep</span> TSTV</span>
+<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb20-1"><a href="#cb20-1" tabindex="-1"></a><span class="ex">$</span> bcftools stats results/vcf/SRR2584866_variants.vcf <span class="kw">|</span> <span class="fu">grep</span> TSTV</span>
 <span id="cb20-2"><a href="#cb20-2" tabindex="-1"></a><span class="co"># TSTV, transitions/transversions:</span></span>
 <span id="cb20-3"><a href="#cb20-3" tabindex="-1"></a><span class="co"># TSTV	[2]id	[3]ts	[4]tv	[5]ts/tv	[6]ts (1st ALT)	[7]tv (1st ALT)	[8]ts/tv (1st ALT)</span></span>
 <span id="cb20-4"><a href="#cb20-4" tabindex="-1"></a><span class="ex">TSTV</span>	0	628	58	10.83	628	58	10.83</span>
@@ -759,7 +759,7 @@ <h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#e
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2">Show me the solution</h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb24">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -876,7 +876,7 @@ <h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#e
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb29">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1083,7 +1083,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://datacarpentry.github.io/wrangling-genomics/04-variant_calling.html",
   "identifier": "https://datacarpentry.github.io/wrangling-genomics/04-variant_calling.html",
   "dateCreated": "2015-03-24",
-  "dateModified": "2023-05-04",
+  "dateModified": "2024-06-14",
   "datePublished": "2024-06-14"
 }
 
diff --git a/05-automation.html b/05-automation.html
index 8c0c8d28..8b3f5218 100644
--- a/05-automation.html
+++ b/05-automation.html
@@ -788,7 +788,7 @@ <h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#e
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb36">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
diff --git a/aio.html b/aio.html
index aa0df60e..a1c6697c 100644
--- a/aio.html
+++ b/aio.html
@@ -765,7 +765,7 @@ <h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#e
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb9">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -983,7 +983,7 @@ <h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#e
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2">Show me the solution</h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb14">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1187,7 +1187,7 @@ <h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#e
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <p>All of the reads contain usable data, but the quality decreases
 toward the end of the reads.</p>
@@ -1460,7 +1460,7 @@ <h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#e
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4">Show me the solution</h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
 <div class="accordion-body">
 <p>We can get the list of all failed tests using <code>grep</code>.</p>
 <div class="codewrapper sourceCode" id="cb42">
@@ -2116,7 +2116,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </div>
 </section></section><section id="aio-04-variant_calling"><p>Content from <a href="04-variant_calling.html">Variant Calling Workflow</a></p>
 <hr>
-<p>Last updated on 2023-05-04 |
+<p>Last updated on 2024-06-14 |
         
         <a href="https://github.com/datacarpentry/wrangling-genomics/edit/main/episodes/04-variant_calling.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
@@ -2207,7 +2207,7 @@ <h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#e
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb2">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -2484,7 +2484,7 @@ <h3 class="callout-title">Filtering<a class="anchor" aria-label="anchor" href="#
 <div class="codewrapper sourceCode" id="cb20">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb20-1"><a href="#cb20-1" tabindex="-1"></a><span class="ex">$</span> bcftools stats results/bcf/SRR2584866_variants.vcf <span class="kw">|</span> <span class="fu">grep</span> TSTV</span>
+<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb20-1"><a href="#cb20-1" tabindex="-1"></a><span class="ex">$</span> bcftools stats results/vcf/SRR2584866_variants.vcf <span class="kw">|</span> <span class="fu">grep</span> TSTV</span>
 <span id="cb20-2"><a href="#cb20-2" tabindex="-1"></a><span class="co"># TSTV, transitions/transversions:</span></span>
 <span id="cb20-3"><a href="#cb20-3" tabindex="-1"></a><span class="co"># TSTV	[2]id	[3]ts	[4]tv	[5]ts/tv	[6]ts (1st ALT)	[7]tv (1st ALT)	[8]ts/tv (1st ALT)</span></span>
 <span id="cb20-4"><a href="#cb20-4" tabindex="-1"></a><span class="ex">TSTV</span>	0	628	58	10.83	628	58	10.83</span>
@@ -2684,7 +2684,7 @@ <h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#e
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2">Show me the solution</h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb24">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -2803,7 +2803,7 @@ <h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#e
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb29">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -3506,7 +3506,7 @@ <h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#e
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb36">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
diff --git a/instructor/02-quality-control.html b/instructor/02-quality-control.html
index 585d6066..2d865fb1 100644
--- a/instructor/02-quality-control.html
+++ b/instructor/02-quality-control.html
@@ -491,7 +491,7 @@ <h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#e
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb9">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -707,7 +707,7 @@ <h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#e
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2">Show me the solution</h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb14">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -910,7 +910,7 @@ <h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#e
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <p>All of the reads contain usable data, but the quality decreases
 toward the end of the reads.</p>
@@ -1178,7 +1178,7 @@ <h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#e
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4">Show me the solution</h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
 <div class="accordion-body">
 <p>We can get the list of all failed tests using <code>grep</code>.</p>
 <div class="codewrapper sourceCode" id="cb42">
diff --git a/instructor/04-variant_calling.html b/instructor/04-variant_calling.html
index 84fd80c5..b3aa1366 100644
--- a/instructor/04-variant_calling.html
+++ b/instructor/04-variant_calling.html
@@ -257,7 +257,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Variant Calling Workflow</h1>
-        <p>Last updated on 2023-05-04 |
+        <p>Last updated on 2024-06-14 |
         
         <a href="https://github.com/datacarpentry/wrangling-genomics/edit/main/episodes/04-variant_calling.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
         
@@ -349,7 +349,7 @@ <h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#e
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
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@@ -618,7 +618,7 @@ <h3 class="callout-title">Filtering<a class="anchor" aria-label="anchor" href="#
 <div class="codewrapper sourceCode" id="cb20">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb20-1"><a href="#cb20-1" tabindex="-1"></a><span class="ex">$</span> bcftools stats results/bcf/SRR2584866_variants.vcf <span class="kw">|</span> <span class="fu">grep</span> TSTV</span>
+<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb20-1"><a href="#cb20-1" tabindex="-1"></a><span class="ex">$</span> bcftools stats results/vcf/SRR2584866_variants.vcf <span class="kw">|</span> <span class="fu">grep</span> TSTV</span>
 <span id="cb20-2"><a href="#cb20-2" tabindex="-1"></a><span class="co"># TSTV, transitions/transversions:</span></span>
 <span id="cb20-3"><a href="#cb20-3" tabindex="-1"></a><span class="co"># TSTV	[2]id	[3]ts	[4]tv	[5]ts/tv	[6]ts (1st ALT)	[7]tv (1st ALT)	[8]ts/tv (1st ALT)</span></span>
 <span id="cb20-4"><a href="#cb20-4" tabindex="-1"></a><span class="ex">TSTV</span>	0	628	58	10.83	628	58	10.83</span>
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 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
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 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
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 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
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 <div class="codewrapper sourceCode" id="cb29">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1085,7 +1085,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://datacarpentry.github.io/wrangling-genomics/instructor/04-variant_calling.html",
   "identifier": "https://datacarpentry.github.io/wrangling-genomics/instructor/04-variant_calling.html",
   "dateCreated": "2015-03-24",
-  "dateModified": "2023-05-04",
+  "dateModified": "2024-06-14",
   "datePublished": "2024-06-14"
 }
 
diff --git a/instructor/05-automation.html b/instructor/05-automation.html
index 367720e7..68bf3383 100644
--- a/instructor/05-automation.html
+++ b/instructor/05-automation.html
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 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb36">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
diff --git a/instructor/aio.html b/instructor/aio.html
index 4e8dab41..6756dd6a 100644
--- a/instructor/aio.html
+++ b/instructor/aio.html
@@ -769,7 +769,7 @@ <h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#e
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
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 <div class="codewrapper sourceCode" id="cb9">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -987,7 +987,7 @@ <h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#e
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2">Show me the solution</h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
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@@ -1191,7 +1191,7 @@ <h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#e
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   <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <p>All of the reads contain usable data, but the quality decreases
 toward the end of the reads.</p>
@@ -1464,7 +1464,7 @@ <h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#e
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4">Show me the solution</h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
 <div class="accordion-body">
 <p>We can get the list of all failed tests using <code>grep</code>.</p>
 <div class="codewrapper sourceCode" id="cb42">
@@ -2121,7 +2121,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
 </div>
 </section></section><section id="aio-04-variant_calling"><p>Content from <a href="04-variant_calling.html">Variant Calling Workflow</a></p>
 <hr>
-<p>Last updated on 2023-05-04 |
+<p>Last updated on 2024-06-14 |
         
         <a href="https://github.com/datacarpentry/wrangling-genomics/edit/main/episodes/04-variant_calling.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 60 minutes</p>
@@ -2213,7 +2213,7 @@ <h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#e
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb2">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -2490,7 +2490,7 @@ <h3 class="callout-title">Filtering<a class="anchor" aria-label="anchor" href="#
 <div class="codewrapper sourceCode" id="cb20">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
 </h3>
-<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb20-1"><a href="#cb20-1" tabindex="-1"></a><span class="ex">$</span> bcftools stats results/bcf/SRR2584866_variants.vcf <span class="kw">|</span> <span class="fu">grep</span> TSTV</span>
+<pre class="sourceCode bash" tabindex="0"><code class="sourceCode bash"><span id="cb20-1"><a href="#cb20-1" tabindex="-1"></a><span class="ex">$</span> bcftools stats results/vcf/SRR2584866_variants.vcf <span class="kw">|</span> <span class="fu">grep</span> TSTV</span>
 <span id="cb20-2"><a href="#cb20-2" tabindex="-1"></a><span class="co"># TSTV, transitions/transversions:</span></span>
 <span id="cb20-3"><a href="#cb20-3" tabindex="-1"></a><span class="co"># TSTV	[2]id	[3]ts	[4]tv	[5]ts/tv	[6]ts (1st ALT)	[7]tv (1st ALT)	[8]ts/tv (1st ALT)</span></span>
 <span id="cb20-4"><a href="#cb20-4" tabindex="-1"></a><span class="ex">TSTV</span>	0	628	58	10.83	628	58	10.83</span>
@@ -2690,7 +2690,7 @@ <h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#e
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2">Show me the solution</h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb24">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -2809,7 +2809,7 @@ <h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#e
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
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 <div class="codewrapper sourceCode" id="cb29">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -3513,7 +3513,7 @@ <h3 class="callout-title">Exercise<a class="anchor" aria-label="anchor" href="#e
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb36">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
diff --git a/md5sum.txt b/md5sum.txt
index e42bc77c..da15c9c1 100644
--- a/md5sum.txt
+++ b/md5sum.txt
@@ -6,7 +6,7 @@
 "episodes/01-background.md" "60fa98ba1e5221d667da0747db2bc484" "site/built/01-background.md" "2023-05-04"
 "episodes/02-quality-control.md" "13d75daa2cbf746a61de8cd4bba5e894" "site/built/02-quality-control.md" "2023-05-04"
 "episodes/03-trimming.md" "15023145f5b83ca995553203934929d7" "site/built/03-trimming.md" "2023-05-04"
-"episodes/04-variant_calling.md" "01bfefb4f2d89bd97e5ddbd6427c2353" "site/built/04-variant_calling.md" "2023-05-04"
+"episodes/04-variant_calling.md" "d4c30bfca92bfe21a15e0cdb6f26f291" "site/built/04-variant_calling.md" "2024-06-14"
 "episodes/05-automation.md" "f5a04ba3cf567ee93e46107ac918ee37" "site/built/05-automation.md" "2024-06-14"
 "instructors/instructor-notes.md" "0d0a7e556fb5a35a198d4c9de6ea4990" "site/built/instructor-notes.md" "2023-05-04"
 "learners/discuss.md" "2758e2e5abd231d82d25c6453d8abbc6" "site/built/discuss.md" "2023-05-04"
diff --git a/pkgdown.yml b/pkgdown.yml
index 9d91b19a..2c752c32 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,5 +2,5 @@ pandoc: 3.1.11
 pkgdown: 2.0.9
 pkgdown_sha: ~
 articles: {}
-last_built: 2024-06-14T19:01Z
+last_built: 2024-06-14T19:03Z