From 9a08526418537210084884c21ad484f842a2f229 Mon Sep 17 00:00:00 2001
From: GitHub Actions <actions@github.com>
Date: Tue, 29 Oct 2024 00:04:17 +0000
Subject: [PATCH] site deploy

Auto-generated via `{sandpaper}`
Source  : 49e4babdf80e77af6a0cb89ad641eb117122f779
Branch  : md-outputs
Author  : GitHub Actions <actions@github.com>
Time    : 2024-07-29 22:06:19 +0000
Message : markdown source builds

Auto-generated via {sandpaper}
Source  : d802ae471450d3bd7ac557f3dc35cf02d8de72d2
Branch  : main
Author  : kerchner@gwu.edu <kerchner@gwu.edu>
Time    : 2024-07-29 22:05:14 +0000
Message : removed libreoffice instructions; updated Windows command line etc. instructions
---
 404.html                         |  4 ++--
 AMI-setup.html                   |  6 +++---
 CODE_OF_CONDUCT.html             |  2 +-
 LICENSE.html                     |  2 +-
 faq.html                         |  2 +-
 index.html                       | 32 ++++++++++++++++----------------
 instructor-notes.html            |  4 ++--
 instructor/404.html              |  4 ++--
 instructor/AMI-setup.html        |  6 +++---
 instructor/CODE_OF_CONDUCT.html  |  2 +-
 instructor/LICENSE.html          |  2 +-
 instructor/faq.html              |  2 +-
 instructor/index.html            | 32 ++++++++++++++++----------------
 instructor/instructor-notes.html |  4 ++--
 instructor/profiles.html         |  4 ++--
 instructor/reference.html        |  2 +-
 instructor/teaching_demos.html   |  2 +-
 pkgdown.yml                      |  2 +-
 profiles.html                    |  4 ++--
 reference.html                   |  2 +-
 teaching_demos.html              |  2 +-
 21 files changed, 61 insertions(+), 61 deletions(-)

diff --git a/404.html b/404.html
index 78507fe..3074523 100644
--- a/404.html
+++ b/404.html
@@ -272,8 +272,8 @@ <h1>Page not found</h1>
   "url": "https://datacarpentry.github.io/genomics-workshop/404.html",
   "identifier": "https://datacarpentry.github.io/genomics-workshop/404.html",
   "dateCreated": "2015-06-03",
-  "dateModified": "2024-10-22",
-  "datePublished": "2024-10-22"
+  "dateModified": "2024-10-29",
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/AMI-setup.html b/AMI-setup.html
index efd43dc..e0a6747 100644
--- a/AMI-setup.html
+++ b/AMI-setup.html
@@ -331,7 +331,7 @@ <h3 class="accordion-header" id="headingSpoiler1">
   Connect to your Amazon Instance (MacOS/Linux)
   </h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
 <div class="accordion-body">
 <ol style="list-style-type: decimal"><li><p>Log into your AWC EC2 Dashboard <a href="https://console.aws.amazon.com/ec2/" class="external-link">https://console.aws.amazon.com/ec2/</a></p></li>
 <li><p>You should see that you have one instance. To proceed, the
@@ -388,7 +388,7 @@ <h3 class="accordion-header" id="headingSpoiler2">
   Connect to your Amazon instance (Windows)
   </h3>
 </button>
-<div id="collapseSpoiler2" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler2" aria-labelledby="headingSpoiler2">
+<div id="collapseSpoiler2" class="accordion-collapse collapse" aria-labelledby="headingSpoiler2" data-bs-parent="#accordionSpoiler2">
 <div class="accordion-body">
 <ol style="list-style-type: decimal"><li><p>Download the PuTTY application at: <a href="https://the.earth.li/~sgtatham/putty/latest/x86/putty.exe" class="external-link">http://the.earth.li/~sgtatham/putty/latest/x86/putty.exe</a></p></li>
 <li><p>Log into your AWC EC2 Dashboard <a href="https://console.aws.amazon.com/ec2/" class="external-link">https://console.aws.amazon.com/ec2/</a></p></li>
@@ -527,7 +527,7 @@ <h3 class="callout-title">Warning</h3>
   "identifier": "https://datacarpentry.github.io/genomics-workshop/AMI-setup.html",
   "dateCreated": "2015-06-03",
   "dateModified": "2023-09-19",
-  "datePublished": "2024-10-22"
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html
index 31fa315..8db316d 100644
--- a/CODE_OF_CONDUCT.html
+++ b/CODE_OF_CONDUCT.html
@@ -300,7 +300,7 @@ <h1>Contributor Code of Conduct</h1>
   "identifier": "https://datacarpentry.github.io/genomics-workshop/CODE_OF_CONDUCT.html",
   "dateCreated": "2015-06-03",
   "dateModified": "2023-09-19",
-  "datePublished": "2024-10-22"
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/LICENSE.html b/LICENSE.html
index a962de8..de6e51e 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -349,7 +349,7 @@ <h1>Licenses</h1>
   "identifier": "https://datacarpentry.github.io/genomics-workshop/LICENSE.html",
   "dateCreated": "2015-06-03",
   "dateModified": "2023-09-19",
-  "datePublished": "2024-10-22"
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/faq.html b/faq.html
index 588860c..d2af56f 100644
--- a/faq.html
+++ b/faq.html
@@ -472,7 +472,7 @@ <h3 id="does-the-aws-image-location-matter-do-i-need-to-set-up-an-ami-in-a-diffe
   "identifier": "https://datacarpentry.github.io/genomics-workshop/faq.html",
   "dateCreated": "2015-06-03",
   "dateModified": "2024-01-08",
-  "datePublished": "2024-10-22"
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/index.html b/index.html
index db360d2..5c7e059 100644
--- a/index.html
+++ b/index.html
@@ -392,7 +392,7 @@ <h3 class="accordion-header" id="headingSpoiler1">
   Windows users only: Setting up software you can use to connect to your cloud computer
   </h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
 <div class="accordion-body">
 <p>Open your Command Prompt app by searching for “cmd”. At the command
 prompt, type <code>ssh</code>. Confirm that this prints out the usage
@@ -524,7 +524,7 @@ <h3 class="accordion-header" id="headingSpoiler2">
   Linux
   </h3>
 </button>
-<div id="collapseSpoiler2" class="accordion-collapse collapse" aria-labelledby="headingSpoiler2" data-bs-parent="#accordionSpoiler2">
+<div id="collapseSpoiler2" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler2" aria-labelledby="headingSpoiler2">
 <div class="accordion-body">
 <p>To install Conda, type:</p>
 <div class="codewrapper sourceCode" id="cb1">
@@ -547,7 +547,7 @@ <h3 class="accordion-header" id="headingSpoiler3">
   MacOS
   </h3>
 </button>
-<div id="collapseSpoiler3" class="accordion-collapse collapse" aria-labelledby="headingSpoiler3" data-bs-parent="#accordionSpoiler3">
+<div id="collapseSpoiler3" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler3" aria-labelledby="headingSpoiler3">
 <div class="accordion-body">
 <p>To install Conda, type:</p>
 <div class="codewrapper sourceCode" id="cb2">
@@ -573,7 +573,7 @@ <h3 class="accordion-header" id="headingSpoiler4">
   MacOS
   </h3>
 </button>
-<div id="collapseSpoiler4" class="accordion-collapse collapse" aria-labelledby="headingSpoiler4" data-bs-parent="#accordionSpoiler4">
+<div id="collapseSpoiler4" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler4" aria-labelledby="headingSpoiler4">
 <div class="accordion-body">
 <p>To install FastQC, type:</p>
 <div class="codewrapper sourceCode" id="cb3">
@@ -593,7 +593,7 @@ <h3 class="accordion-header" id="headingSpoiler5">
   FastQC Source Code Installation
   </h3>
 </button>
-<div id="collapseSpoiler5" class="accordion-collapse collapse" aria-labelledby="headingSpoiler5" data-bs-parent="#accordionSpoiler5">
+<div id="collapseSpoiler5" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler5" aria-labelledby="headingSpoiler5">
 <div class="accordion-body">
 <p>If you prefer to install from source, follow the directions
 below:</p>
@@ -639,7 +639,7 @@ <h3 class="accordion-header" id="headingSpoiler6">
   MacOS
   </h3>
 </button>
-<div id="collapseSpoiler6" class="accordion-collapse collapse" aria-labelledby="headingSpoiler6" data-bs-parent="#accordionSpoiler6">
+<div id="collapseSpoiler6" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler6" aria-labelledby="headingSpoiler6">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb8">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -658,7 +658,7 @@ <h3 class="accordion-header" id="headingSpoiler7">
   Trimmomatic Source Code Installation
   </h3>
 </button>
-<div id="collapseSpoiler7" class="accordion-collapse collapse" aria-labelledby="headingSpoiler7" data-bs-parent="#accordionSpoiler7">
+<div id="collapseSpoiler7" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler7" aria-labelledby="headingSpoiler7">
 <div class="accordion-body">
 <p>If you prefer to install from source, follow the directions
 below:</p>
@@ -697,7 +697,7 @@ <h3 class="accordion-header" id="headingSpoiler8">
   Simplify the Invocation, or to Test your installation if you installed with miniconda3:
   </h3>
 </button>
-<div id="collapseSpoiler8" class="accordion-collapse collapse" aria-labelledby="headingSpoiler8" data-bs-parent="#accordionSpoiler8">
+<div id="collapseSpoiler8" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler8" aria-labelledby="headingSpoiler8">
 <div class="accordion-body">
 <p>To simplify the invocation you could also create a script in the
 ~/bin folder:</p>
@@ -729,7 +729,7 @@ <h3 class="accordion-header" id="headingSpoiler9">
   MacOS
   </h3>
 </button>
-<div id="collapseSpoiler9" class="accordion-collapse collapse" aria-labelledby="headingSpoiler9" data-bs-parent="#accordionSpoiler9">
+<div id="collapseSpoiler9" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler9" aria-labelledby="headingSpoiler9">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb15">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -748,7 +748,7 @@ <h3 class="accordion-header" id="headingSpoiler10">
   BWA Source Code Installation
   </h3>
 </button>
-<div id="collapseSpoiler10" class="accordion-collapse collapse" aria-labelledby="headingSpoiler10" data-bs-parent="#accordionSpoiler10">
+<div id="collapseSpoiler10" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler10" aria-labelledby="headingSpoiler10">
 <div class="accordion-body">
 <p>If you prefer to install from source, follow the instructions
 below:</p>
@@ -783,7 +783,7 @@ <h3 class="accordion-header" id="headingSpoiler11">
   MacOS
   </h3>
 </button>
-<div id="collapseSpoiler11" class="accordion-collapse collapse" aria-labelledby="headingSpoiler11" data-bs-parent="#accordionSpoiler11">
+<div id="collapseSpoiler11" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler11" aria-labelledby="headingSpoiler11">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb18">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -817,7 +817,7 @@ <h3 class="accordion-header" id="headingSpoiler12">
   SAMtools Source Code Installation
   </h3>
 </button>
-<div id="collapseSpoiler12" class="accordion-collapse collapse" aria-labelledby="headingSpoiler12" data-bs-parent="#accordionSpoiler12">
+<div id="collapseSpoiler12" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler12" aria-labelledby="headingSpoiler12">
 <div class="accordion-body">
 <p>If you prefer to install from source, follow the instructions
 below:</p>
@@ -858,7 +858,7 @@ <h3 class="accordion-header" id="headingSpoiler13">
   MacOS
   </h3>
 </button>
-<div id="collapseSpoiler13" class="accordion-collapse collapse" aria-labelledby="headingSpoiler13" data-bs-parent="#accordionSpoiler13">
+<div id="collapseSpoiler13" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler13" aria-labelledby="headingSpoiler13">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb22">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -877,7 +877,7 @@ <h3 class="accordion-header" id="headingSpoiler14">
   BCF tools Source Code Installation
   </h3>
 </button>
-<div id="collapseSpoiler14" class="accordion-collapse collapse" aria-labelledby="headingSpoiler14" data-bs-parent="#accordionSpoiler14">
+<div id="collapseSpoiler14" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler14" aria-labelledby="headingSpoiler14">
 <div class="accordion-body">
 <p>If you prefer to install from source, follow the instructions
 below:</p>
@@ -961,8 +961,8 @@ <h3 id="igv">IGV<a class="anchor" aria-label="anchor" href="#igv"></a></h3>
   "url": "https://datacarpentry.github.io/genomics-workshop/index.html",
   "identifier": "https://datacarpentry.github.io/genomics-workshop/index.html",
   "dateCreated": "2015-06-03",
-  "dateModified": "2024-10-22",
-  "datePublished": "2024-10-22"
+  "dateModified": "2024-10-29",
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/instructor-notes.html b/instructor-notes.html
index 60aa5f3..6ffa3ed 100644
--- a/instructor-notes.html
+++ b/instructor-notes.html
@@ -296,8 +296,8 @@ <h4 id="installation">Installation<a class="anchor" aria-label="anchor" href="#i
   "url": "https://datacarpentry.github.io/genomics-workshop/instructor-notes.html",
   "identifier": "https://datacarpentry.github.io/genomics-workshop/instructor-notes.html",
   "dateCreated": "2015-06-03",
-  "dateModified": "2024-10-22",
-  "datePublished": "2024-10-22"
+  "dateModified": "2024-10-29",
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/instructor/404.html b/instructor/404.html
index 4806278..b648ac2 100644
--- a/instructor/404.html
+++ b/instructor/404.html
@@ -266,8 +266,8 @@ <h1>Page not found</h1>
   "url": "https://datacarpentry.github.io/genomics-workshop/instructor/404.html",
   "identifier": "https://datacarpentry.github.io/genomics-workshop/instructor/404.html",
   "dateCreated": "2015-06-03",
-  "dateModified": "2024-10-22",
-  "datePublished": "2024-10-22"
+  "dateModified": "2024-10-29",
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/instructor/AMI-setup.html b/instructor/AMI-setup.html
index ddcb922..89e1046 100644
--- a/instructor/AMI-setup.html
+++ b/instructor/AMI-setup.html
@@ -327,7 +327,7 @@ <h3 class="accordion-header" id="headingSpoiler1">
   Connect to your Amazon Instance (MacOS/Linux)
   </h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
 <div class="accordion-body">
 <ol style="list-style-type: decimal"><li><p>Log into your AWC EC2 Dashboard <a href="https://console.aws.amazon.com/ec2/" class="external-link">https://console.aws.amazon.com/ec2/</a></p></li>
 <li><p>You should see that you have one instance. To proceed, the
@@ -384,7 +384,7 @@ <h3 class="accordion-header" id="headingSpoiler2">
   Connect to your Amazon instance (Windows)
   </h3>
 </button>
-<div id="collapseSpoiler2" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler2" aria-labelledby="headingSpoiler2">
+<div id="collapseSpoiler2" class="accordion-collapse collapse" aria-labelledby="headingSpoiler2" data-bs-parent="#accordionSpoiler2">
 <div class="accordion-body">
 <ol style="list-style-type: decimal"><li><p>Download the PuTTY application at: <a href="https://the.earth.li/~sgtatham/putty/latest/x86/putty.exe" class="external-link">http://the.earth.li/~sgtatham/putty/latest/x86/putty.exe</a></p></li>
 <li><p>Log into your AWC EC2 Dashboard <a href="https://console.aws.amazon.com/ec2/" class="external-link">https://console.aws.amazon.com/ec2/</a></p></li>
@@ -523,7 +523,7 @@ <h3 class="callout-title">Warning</h3>
   "identifier": "https://datacarpentry.github.io/genomics-workshop/instructor/AMI-setup.html",
   "dateCreated": "2015-06-03",
   "dateModified": "2023-09-19",
-  "datePublished": "2024-10-22"
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/instructor/CODE_OF_CONDUCT.html b/instructor/CODE_OF_CONDUCT.html
index 5a4567d..80f3ed1 100644
--- a/instructor/CODE_OF_CONDUCT.html
+++ b/instructor/CODE_OF_CONDUCT.html
@@ -296,7 +296,7 @@ <h1>Contributor Code of Conduct</h1>
   "identifier": "https://datacarpentry.github.io/genomics-workshop/instructor/CODE_OF_CONDUCT.html",
   "dateCreated": "2015-06-03",
   "dateModified": "2023-09-19",
-  "datePublished": "2024-10-22"
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/instructor/LICENSE.html b/instructor/LICENSE.html
index 8d449d9..e598caa 100644
--- a/instructor/LICENSE.html
+++ b/instructor/LICENSE.html
@@ -345,7 +345,7 @@ <h1>Licenses</h1>
   "identifier": "https://datacarpentry.github.io/genomics-workshop/instructor/LICENSE.html",
   "dateCreated": "2015-06-03",
   "dateModified": "2023-09-19",
-  "datePublished": "2024-10-22"
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/instructor/faq.html b/instructor/faq.html
index 82365d1..36794f3 100644
--- a/instructor/faq.html
+++ b/instructor/faq.html
@@ -468,7 +468,7 @@ <h3 id="does-the-aws-image-location-matter-do-i-need-to-set-up-an-ami-in-a-diffe
   "identifier": "https://datacarpentry.github.io/genomics-workshop/instructor/faq.html",
   "dateCreated": "2015-06-03",
   "dateModified": "2024-01-08",
-  "datePublished": "2024-10-22"
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/instructor/index.html b/instructor/index.html
index b9eb81a..52590e5 100644
--- a/instructor/index.html
+++ b/instructor/index.html
@@ -391,7 +391,7 @@ <h3 class="accordion-header" id="headingSpoiler1">
   Windows users only: Setting up software you can use to connect to your cloud computer
   </h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
 <div class="accordion-body">
 <p>Open your Command Prompt app by searching for “cmd”. At the command
 prompt, type <code>ssh</code>. Confirm that this prints out the usage
@@ -523,7 +523,7 @@ <h3 class="accordion-header" id="headingSpoiler2">
   Linux
   </h3>
 </button>
-<div id="collapseSpoiler2" class="accordion-collapse collapse" aria-labelledby="headingSpoiler2" data-bs-parent="#accordionSpoiler2">
+<div id="collapseSpoiler2" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler2" aria-labelledby="headingSpoiler2">
 <div class="accordion-body">
 <p>To install Conda, type:</p>
 <div class="codewrapper sourceCode" id="cb1">
@@ -546,7 +546,7 @@ <h3 class="accordion-header" id="headingSpoiler3">
   MacOS
   </h3>
 </button>
-<div id="collapseSpoiler3" class="accordion-collapse collapse" aria-labelledby="headingSpoiler3" data-bs-parent="#accordionSpoiler3">
+<div id="collapseSpoiler3" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler3" aria-labelledby="headingSpoiler3">
 <div class="accordion-body">
 <p>To install Conda, type:</p>
 <div class="codewrapper sourceCode" id="cb2">
@@ -572,7 +572,7 @@ <h3 class="accordion-header" id="headingSpoiler4">
   MacOS
   </h3>
 </button>
-<div id="collapseSpoiler4" class="accordion-collapse collapse" aria-labelledby="headingSpoiler4" data-bs-parent="#accordionSpoiler4">
+<div id="collapseSpoiler4" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler4" aria-labelledby="headingSpoiler4">
 <div class="accordion-body">
 <p>To install FastQC, type:</p>
 <div class="codewrapper sourceCode" id="cb3">
@@ -592,7 +592,7 @@ <h3 class="accordion-header" id="headingSpoiler5">
   FastQC Source Code Installation
   </h3>
 </button>
-<div id="collapseSpoiler5" class="accordion-collapse collapse" aria-labelledby="headingSpoiler5" data-bs-parent="#accordionSpoiler5">
+<div id="collapseSpoiler5" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler5" aria-labelledby="headingSpoiler5">
 <div class="accordion-body">
 <p>If you prefer to install from source, follow the directions
 below:</p>
@@ -638,7 +638,7 @@ <h3 class="accordion-header" id="headingSpoiler6">
   MacOS
   </h3>
 </button>
-<div id="collapseSpoiler6" class="accordion-collapse collapse" aria-labelledby="headingSpoiler6" data-bs-parent="#accordionSpoiler6">
+<div id="collapseSpoiler6" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler6" aria-labelledby="headingSpoiler6">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb8">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -657,7 +657,7 @@ <h3 class="accordion-header" id="headingSpoiler7">
   Trimmomatic Source Code Installation
   </h3>
 </button>
-<div id="collapseSpoiler7" class="accordion-collapse collapse" aria-labelledby="headingSpoiler7" data-bs-parent="#accordionSpoiler7">
+<div id="collapseSpoiler7" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler7" aria-labelledby="headingSpoiler7">
 <div class="accordion-body">
 <p>If you prefer to install from source, follow the directions
 below:</p>
@@ -696,7 +696,7 @@ <h3 class="accordion-header" id="headingSpoiler8">
   Simplify the Invocation, or to Test your installation if you installed with miniconda3:
   </h3>
 </button>
-<div id="collapseSpoiler8" class="accordion-collapse collapse" aria-labelledby="headingSpoiler8" data-bs-parent="#accordionSpoiler8">
+<div id="collapseSpoiler8" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler8" aria-labelledby="headingSpoiler8">
 <div class="accordion-body">
 <p>To simplify the invocation you could also create a script in the
 ~/bin folder:</p>
@@ -728,7 +728,7 @@ <h3 class="accordion-header" id="headingSpoiler9">
   MacOS
   </h3>
 </button>
-<div id="collapseSpoiler9" class="accordion-collapse collapse" aria-labelledby="headingSpoiler9" data-bs-parent="#accordionSpoiler9">
+<div id="collapseSpoiler9" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler9" aria-labelledby="headingSpoiler9">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb15">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -747,7 +747,7 @@ <h3 class="accordion-header" id="headingSpoiler10">
   BWA Source Code Installation
   </h3>
 </button>
-<div id="collapseSpoiler10" class="accordion-collapse collapse" aria-labelledby="headingSpoiler10" data-bs-parent="#accordionSpoiler10">
+<div id="collapseSpoiler10" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler10" aria-labelledby="headingSpoiler10">
 <div class="accordion-body">
 <p>If you prefer to install from source, follow the instructions
 below:</p>
@@ -782,7 +782,7 @@ <h3 class="accordion-header" id="headingSpoiler11">
   MacOS
   </h3>
 </button>
-<div id="collapseSpoiler11" class="accordion-collapse collapse" aria-labelledby="headingSpoiler11" data-bs-parent="#accordionSpoiler11">
+<div id="collapseSpoiler11" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler11" aria-labelledby="headingSpoiler11">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb18">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -816,7 +816,7 @@ <h3 class="accordion-header" id="headingSpoiler12">
   SAMtools Source Code Installation
   </h3>
 </button>
-<div id="collapseSpoiler12" class="accordion-collapse collapse" aria-labelledby="headingSpoiler12" data-bs-parent="#accordionSpoiler12">
+<div id="collapseSpoiler12" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler12" aria-labelledby="headingSpoiler12">
 <div class="accordion-body">
 <p>If you prefer to install from source, follow the instructions
 below:</p>
@@ -857,7 +857,7 @@ <h3 class="accordion-header" id="headingSpoiler13">
   MacOS
   </h3>
 </button>
-<div id="collapseSpoiler13" class="accordion-collapse collapse" aria-labelledby="headingSpoiler13" data-bs-parent="#accordionSpoiler13">
+<div id="collapseSpoiler13" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler13" aria-labelledby="headingSpoiler13">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb22">
 <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="accordion-header" id="headingSpoiler14">
   BCF tools Source Code Installation
   </h3>
 </button>
-<div id="collapseSpoiler14" class="accordion-collapse collapse" aria-labelledby="headingSpoiler14" data-bs-parent="#accordionSpoiler14">
+<div id="collapseSpoiler14" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler14" aria-labelledby="headingSpoiler14">
 <div class="accordion-body">
 <p>If you prefer to install from source, follow the instructions
 below:</p>
@@ -960,8 +960,8 @@ <h3 id="igv">IGV<a class="anchor" aria-label="anchor" href="#igv"></a></h3>
   "url": "https://datacarpentry.github.io/genomics-workshop/instructor/index.html",
   "identifier": "https://datacarpentry.github.io/genomics-workshop/instructor/index.html",
   "dateCreated": "2015-06-03",
-  "dateModified": "2024-10-22",
-  "datePublished": "2024-10-22"
+  "dateModified": "2024-10-29",
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/instructor/instructor-notes.html b/instructor/instructor-notes.html
index 097cfdc..8111d2b 100644
--- a/instructor/instructor-notes.html
+++ b/instructor/instructor-notes.html
@@ -290,8 +290,8 @@ <h4 id="installation">Installation<a class="anchor" aria-label="anchor" href="#i
   "url": "https://datacarpentry.github.io/genomics-workshop/instructor/instructor-notes.html",
   "identifier": "https://datacarpentry.github.io/genomics-workshop/instructor/instructor-notes.html",
   "dateCreated": "2015-06-03",
-  "dateModified": "2024-10-22",
-  "datePublished": "2024-10-22"
+  "dateModified": "2024-10-29",
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/instructor/profiles.html b/instructor/profiles.html
index 9c52b97..6d741d0 100644
--- a/instructor/profiles.html
+++ b/instructor/profiles.html
@@ -254,8 +254,8 @@ <h1>Learner Profiles</h1>
   "url": "https://datacarpentry.github.io/genomics-workshop/instructor/profiles.html",
   "identifier": "https://datacarpentry.github.io/genomics-workshop/instructor/profiles.html",
   "dateCreated": "2015-06-03",
-  "dateModified": "2024-10-22",
-  "datePublished": "2024-10-22"
+  "dateModified": "2024-10-29",
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/instructor/reference.html b/instructor/reference.html
index 1597e23..e69b14d 100644
--- a/instructor/reference.html
+++ b/instructor/reference.html
@@ -288,7 +288,7 @@ <h1>Glossary</h1>
   "identifier": "https://datacarpentry.github.io/genomics-workshop/instructor/reference.html",
   "dateCreated": "2015-06-03",
   "dateModified": "2023-09-19",
-  "datePublished": "2024-10-22"
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/instructor/teaching_demos.html b/instructor/teaching_demos.html
index fe6480d..bce2fe3 100644
--- a/instructor/teaching_demos.html
+++ b/instructor/teaching_demos.html
@@ -344,7 +344,7 @@ <h4 id="data-analysis-and-visualization-in-r"><a href="https://datacarpentry.org
   "identifier": "https://datacarpentry.github.io/genomics-workshop/instructor/teaching_demos.html",
   "dateCreated": "2015-06-03",
   "dateModified": "2023-10-02",
-  "datePublished": "2024-10-22"
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/pkgdown.yml b/pkgdown.yml
index f2a41d1..427190d 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,4 +2,4 @@ pandoc: 3.1.11
 pkgdown: 2.1.1
 pkgdown_sha: ~
 articles: {}
-last_built: 2024-10-22T00:04Z
+last_built: 2024-10-29T00:04Z
diff --git a/profiles.html b/profiles.html
index f4137ab..e48d2ac 100644
--- a/profiles.html
+++ b/profiles.html
@@ -260,8 +260,8 @@ <h1>Learner Profiles</h1>
   "url": "https://datacarpentry.github.io/genomics-workshop/profiles.html",
   "identifier": "https://datacarpentry.github.io/genomics-workshop/profiles.html",
   "dateCreated": "2015-06-03",
-  "dateModified": "2024-10-22",
-  "datePublished": "2024-10-22"
+  "dateModified": "2024-10-29",
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/reference.html b/reference.html
index 502e21d..7f56770 100644
--- a/reference.html
+++ b/reference.html
@@ -292,7 +292,7 @@ <h1>Glossary</h1>
   "identifier": "https://datacarpentry.github.io/genomics-workshop/reference.html",
   "dateCreated": "2015-06-03",
   "dateModified": "2023-09-19",
-  "datePublished": "2024-10-22"
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/teaching_demos.html b/teaching_demos.html
index c826214..23d87d3 100644
--- a/teaching_demos.html
+++ b/teaching_demos.html
@@ -348,7 +348,7 @@ <h4 id="data-analysis-and-visualization-in-r"><a href="https://datacarpentry.org
   "identifier": "https://datacarpentry.github.io/genomics-workshop/teaching_demos.html",
   "dateCreated": "2015-06-03",
   "dateModified": "2023-10-02",
-  "datePublished": "2024-10-22"
+  "datePublished": "2024-10-29"
 }
 
   </script><script>