From a34330f160e21185182ff299f3f73500910257d0 Mon Sep 17 00:00:00 2001
From: GitHub Actions <actions@github.com>
Date: Sat, 13 Jul 2024 15:35:20 +0000
Subject: [PATCH] site deploy

Auto-generated via {sandpaper}
Source  : 628177b6c38840c44ff558bf45fb3fd5aae406fa
Branch  : md-outputs
Author  : GitHub Actions <actions@github.com>
Time    : 2024-07-13 15:35:10 +0000
Message : markdown source builds

Auto-generated via {sandpaper}
Source  : 69af2577296499ce04035ed5047f2dd06a9cce49
Branch  : main
Author  : Travis Wrightsman <travis@wrightsman.org>
Time    : 2024-07-13 15:34:18 +0000
Message : Merge pull request #156 from datacarpentry/sheraaronhurt-patch-1

Update who sends AWS.md
---
 404.html                         |  4 ++--
 AMI-setup.html                   |  6 +++---
 CODE_OF_CONDUCT.html             |  2 +-
 LICENSE.html                     |  2 +-
 faq.html                         |  8 +++----
 index.html                       | 36 ++++++++++++++++----------------
 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              |  8 +++----
 instructor/index.html            | 36 ++++++++++++++++----------------
 instructor/instructor-notes.html |  4 ++--
 instructor/profiles.html         |  4 ++--
 instructor/reference.html        |  2 +-
 instructor/teaching_demos.html   |  2 +-
 md5sum.txt                       |  2 +-
 pkgdown.yml                      |  2 +-
 profiles.html                    |  4 ++--
 reference.html                   |  2 +-
 teaching_demos.html              |  2 +-
 22 files changed, 72 insertions(+), 72 deletions(-)

diff --git a/404.html b/404.html
index a6d1bf2d..9ec8da66 100644
--- a/404.html
+++ b/404.html
@@ -273,8 +273,8 @@ <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": "2024-07-09",
-  "datePublished": "2024-07-09"
+  "dateModified": "2024-07-13",
+  "datePublished": "2024-07-13"
 }
 
   </script><script>
diff --git a/AMI-setup.html b/AMI-setup.html
index 9e22755a..4abc7a32 100644
--- a/AMI-setup.html
+++ b/AMI-setup.html
@@ -333,7 +333,7 @@ <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
@@ -390,7 +390,7 @@ <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>
@@ -531,7 +531,7 @@ <h3 class="callout-title">Warning<a class="anchor" aria-label="anchor" href="#wa
   "identifier": "https://datacarpentry.github.io/genomics-workshop/AMI-setup.html",
   "dateCreated": "2015-06-03",
   "dateModified": "2023-09-19",
-  "datePublished": "2024-07-09"
+  "datePublished": "2024-07-13"
 }
 
   </script><script>
diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html
index b71e44e5..e7c03e20 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": "2024-07-09"
+  "datePublished": "2024-07-13"
 }
 
   </script><script>
diff --git a/LICENSE.html b/LICENSE.html
index ac0853df..4c7966a2 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -352,7 +352,7 @@ <h1>Licenses</h1>
   "identifier": "https://datacarpentry.github.io/genomics-workshop/LICENSE.html",
   "dateCreated": "2015-06-03",
   "dateModified": "2023-09-19",
-  "datePublished": "2024-07-09"
+  "datePublished": "2024-07-13"
 }
 
   </script><script>
diff --git a/faq.html b/faq.html
index b8ec8e15..5ab79103 100644
--- a/faq.html
+++ b/faq.html
@@ -220,7 +220,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Frequently Asked Questions</h1>
-        <p>Last updated on 2024-01-08 |
+        <p>Last updated on 2024-07-13 |
 
         <a href="https://github.com/datacarpentry/genomics-workshop/edit/main/instructors/faq.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 
@@ -368,7 +368,7 @@ <h3 id="when-will-i-have-access-to-an-aws-image-to-practice-on">When will I have
 </div>
 <div class="section level3">
 <h3 id="how-will-my-learners-get-connection-and-log-in-information">How will my learners get connection and log-in information?<a class="anchor" aria-label="anchor" href="#how-will-my-learners-get-connection-and-log-in-information"></a></h3>
-<p>The Carpentries Workshop and Logistics Manager will provide
+<p>The Carpentries Workshops and Instruction Team will provide
 Instructors with connection information for AMI instances the day before
 the workshop. Enough instances will be provided for each learner, and if
 requested, for each workshop helper, to have their own individual
@@ -473,8 +473,8 @@ <h3 id="does-the-aws-image-location-matter-do-i-need-to-set-up-an-ami-in-a-diffe
   "url": "https://datacarpentry.github.io/genomics-workshop/faq.html",
   "identifier": "https://datacarpentry.github.io/genomics-workshop/faq.html",
   "dateCreated": "2015-06-03",
-  "dateModified": "2024-01-08",
-  "datePublished": "2024-07-09"
+  "dateModified": "2024-07-13",
+  "datePublished": "2024-07-13"
 }
 
   </script><script>
diff --git a/index.html b/index.html
index 3774c708..2e6c2973 100644
--- a/index.html
+++ b/index.html
@@ -399,7 +399,7 @@ <h3 class="accordion-header" id="headingSpoiler1">
   Windows
   </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">
 <ul><li>Visit <a href="https://www.libreoffice.org/download/libreoffice-fresh/" class="external-link">the
 LibreOffice installation page</a>. The version for Windows should
@@ -479,7 +479,7 @@ <h3 class="accordion-header" id="headingSpoiler2">
   Mac OS X
   </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">
 <ul><li>Visit <a href="https://www.libreoffice.org/download/libreoffice-fresh/" class="external-link">the
 LibreOffice installation page</a>. The version for Mac should
@@ -501,7 +501,7 @@ <h3 class="accordion-header" id="headingSpoiler3">
   Linux
   </h3>
 </button>
-<div id="collapseSpoiler3" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler3" aria-labelledby="headingSpoiler3">
+<div id="collapseSpoiler3" class="accordion-collapse collapse" aria-labelledby="headingSpoiler3" data-bs-parent="#accordionSpoiler3">
 <div class="accordion-body">
 <ul><li>Visit <a href="https://www.libreoffice.org/download/libreoffice-fresh/" class="external-link">the
 LibreOffice installation page</a>. The version for Linux should
@@ -621,7 +621,7 @@ <h3 class="accordion-header" id="headingSpoiler4">
   Linux
   </h3>
 </button>
-<div id="collapseSpoiler4" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler4" aria-labelledby="headingSpoiler4">
+<div id="collapseSpoiler4" class="accordion-collapse collapse" aria-labelledby="headingSpoiler4" data-bs-parent="#accordionSpoiler4">
 <div class="accordion-body">
 <p>To install Conda, type:</p>
 <div class="codewrapper sourceCode" id="cb1">
@@ -644,7 +644,7 @@ <h3 class="accordion-header" id="headingSpoiler5">
   MacOS
   </h3>
 </button>
-<div id="collapseSpoiler5" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler5" aria-labelledby="headingSpoiler5">
+<div id="collapseSpoiler5" class="accordion-collapse collapse" aria-labelledby="headingSpoiler5" data-bs-parent="#accordionSpoiler5">
 <div class="accordion-body">
 <p>To install Conda, type:</p>
 <div class="codewrapper sourceCode" id="cb2">
@@ -670,7 +670,7 @@ <h3 class="accordion-header" id="headingSpoiler6">
   MacOS
   </h3>
 </button>
-<div id="collapseSpoiler6" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler6" aria-labelledby="headingSpoiler6">
+<div id="collapseSpoiler6" class="accordion-collapse collapse" aria-labelledby="headingSpoiler6" data-bs-parent="#accordionSpoiler6">
 <div class="accordion-body">
 <p>To install FastQC, type:</p>
 <div class="codewrapper sourceCode" id="cb3">
@@ -690,7 +690,7 @@ <h3 class="accordion-header" id="headingSpoiler7">
   FastQC Source Code Installation
   </h3>
 </button>
-<div id="collapseSpoiler7" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler7" aria-labelledby="headingSpoiler7">
+<div id="collapseSpoiler7" class="accordion-collapse collapse" aria-labelledby="headingSpoiler7" data-bs-parent="#accordionSpoiler7">
 <div class="accordion-body">
 <p>If you prefer to install from source, follow the directions
 below:</p>
@@ -736,7 +736,7 @@ <h3 class="accordion-header" id="headingSpoiler8">
   MacOS
   </h3>
 </button>
-<div id="collapseSpoiler8" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler8" aria-labelledby="headingSpoiler8">
+<div id="collapseSpoiler8" class="accordion-collapse collapse" aria-labelledby="headingSpoiler8" data-bs-parent="#accordionSpoiler8">
 <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>
@@ -755,7 +755,7 @@ <h3 class="accordion-header" id="headingSpoiler9">
   Trimmomatic Source Code Installation
   </h3>
 </button>
-<div id="collapseSpoiler9" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler9" aria-labelledby="headingSpoiler9">
+<div id="collapseSpoiler9" class="accordion-collapse collapse" aria-labelledby="headingSpoiler9" data-bs-parent="#accordionSpoiler9">
 <div class="accordion-body">
 <p>If you prefer to install from source, follow the directions
 below:</p>
@@ -794,7 +794,7 @@ <h3 class="accordion-header" id="headingSpoiler10">
   Simplify the Invocation, or to Test your installation if you installed with miniconda3:
   </h3>
 </button>
-<div id="collapseSpoiler10" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler10" aria-labelledby="headingSpoiler10">
+<div id="collapseSpoiler10" class="accordion-collapse collapse" aria-labelledby="headingSpoiler10" data-bs-parent="#accordionSpoiler10">
 <div class="accordion-body">
 <p>To simplify the invocation you could also create a script in the
 ~/bin folder:</p>
@@ -826,7 +826,7 @@ <h3 class="accordion-header" id="headingSpoiler11">
   MacOS
   </h3>
 </button>
-<div id="collapseSpoiler11" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler11" aria-labelledby="headingSpoiler11">
+<div id="collapseSpoiler11" class="accordion-collapse collapse" aria-labelledby="headingSpoiler11" data-bs-parent="#accordionSpoiler11">
 <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>
@@ -845,7 +845,7 @@ <h3 class="accordion-header" id="headingSpoiler12">
   BWA Source Code Installation
   </h3>
 </button>
-<div id="collapseSpoiler12" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler12" aria-labelledby="headingSpoiler12">
+<div id="collapseSpoiler12" class="accordion-collapse collapse" aria-labelledby="headingSpoiler12" data-bs-parent="#accordionSpoiler12">
 <div class="accordion-body">
 <p>If you prefer to install from source, follow the instructions
 below:</p>
@@ -880,7 +880,7 @@ <h3 class="accordion-header" id="headingSpoiler13">
   MacOS
   </h3>
 </button>
-<div id="collapseSpoiler13" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler13" aria-labelledby="headingSpoiler13">
+<div id="collapseSpoiler13" class="accordion-collapse collapse" aria-labelledby="headingSpoiler13" data-bs-parent="#accordionSpoiler13">
 <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>
@@ -915,7 +915,7 @@ <h3 class="accordion-header" id="headingSpoiler14">
   SAMtools Source Code Installation
   </h3>
 </button>
-<div id="collapseSpoiler14" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler14" aria-labelledby="headingSpoiler14">
+<div id="collapseSpoiler14" class="accordion-collapse collapse" aria-labelledby="headingSpoiler14" data-bs-parent="#accordionSpoiler14">
 <div class="accordion-body">
 <p>If you prefer to install from source, follow the instructions
 below:</p>
@@ -956,7 +956,7 @@ <h3 class="accordion-header" id="headingSpoiler15">
   MacOS
   </h3>
 </button>
-<div id="collapseSpoiler15" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler15" aria-labelledby="headingSpoiler15">
+<div id="collapseSpoiler15" class="accordion-collapse collapse" aria-labelledby="headingSpoiler15" data-bs-parent="#accordionSpoiler15">
 <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>
@@ -975,7 +975,7 @@ <h3 class="accordion-header" id="headingSpoiler16">
   BCF tools Source Code Installation
   </h3>
 </button>
-<div id="collapseSpoiler16" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler16" aria-labelledby="headingSpoiler16">
+<div id="collapseSpoiler16" class="accordion-collapse collapse" aria-labelledby="headingSpoiler16" data-bs-parent="#accordionSpoiler16">
 <div class="accordion-body">
 <p>If you prefer to install from source, follow the instructions
 below:</p>
@@ -1059,8 +1059,8 @@ <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": "2024-07-09",
-  "datePublished": "2024-07-09"
+  "dateModified": "2024-07-13",
+  "datePublished": "2024-07-13"
 }
 
   </script><script>
diff --git a/instructor-notes.html b/instructor-notes.html
index 3e3a307d..70b1ba43 100644
--- a/instructor-notes.html
+++ b/instructor-notes.html
@@ -300,8 +300,8 @@ <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": "2024-07-09",
-  "datePublished": "2024-07-09"
+  "dateModified": "2024-07-13",
+  "datePublished": "2024-07-13"
 }
 
   </script><script>
diff --git a/instructor/404.html b/instructor/404.html
index 8a5033b5..f76121ff 100644
--- a/instructor/404.html
+++ b/instructor/404.html
@@ -267,8 +267,8 @@ <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": "2024-07-09",
-  "datePublished": "2024-07-09"
+  "dateModified": "2024-07-13",
+  "datePublished": "2024-07-13"
 }
 
   </script><script>
diff --git a/instructor/AMI-setup.html b/instructor/AMI-setup.html
index 640ad72a..6db0b4c2 100644
--- a/instructor/AMI-setup.html
+++ b/instructor/AMI-setup.html
@@ -329,7 +329,7 @@ <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
@@ -386,7 +386,7 @@ <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<a class="anchor" aria-label="anchor" href="#wa
   "identifier": "https://datacarpentry.github.io/genomics-workshop/instructor/AMI-setup.html",
   "dateCreated": "2015-06-03",
   "dateModified": "2023-09-19",
-  "datePublished": "2024-07-09"
+  "datePublished": "2024-07-13"
 }
 
   </script><script>
diff --git a/instructor/CODE_OF_CONDUCT.html b/instructor/CODE_OF_CONDUCT.html
index 01ca3b8e..2e5b68e9 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": "2024-07-09"
+  "datePublished": "2024-07-13"
 }
 
   </script><script>
diff --git a/instructor/LICENSE.html b/instructor/LICENSE.html
index bd40813e..ccd36ac5 100644
--- a/instructor/LICENSE.html
+++ b/instructor/LICENSE.html
@@ -348,7 +348,7 @@ <h1>Licenses</h1>
   "identifier": "https://datacarpentry.github.io/genomics-workshop/instructor/LICENSE.html",
   "dateCreated": "2015-06-03",
   "dateModified": "2023-09-19",
-  "datePublished": "2024-07-09"
+  "datePublished": "2024-07-13"
 }
 
   </script><script>
diff --git a/instructor/faq.html b/instructor/faq.html
index 7ef81849..ca347998 100644
--- a/instructor/faq.html
+++ b/instructor/faq.html
@@ -214,7 +214,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Frequently Asked Questions</h1>
-        <p>Last updated on 2024-01-08 |
+        <p>Last updated on 2024-07-13 |
 
         <a href="https://github.com/datacarpentry/genomics-workshop/edit/main/instructors/faq.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 
@@ -364,7 +364,7 @@ <h3 id="when-will-i-have-access-to-an-aws-image-to-practice-on">When will I have
 </div>
 <div class="section level3">
 <h3 id="how-will-my-learners-get-connection-and-log-in-information">How will my learners get connection and log-in information?<a class="anchor" aria-label="anchor" href="#how-will-my-learners-get-connection-and-log-in-information"></a></h3>
-<p>The Carpentries Workshop and Logistics Manager will provide
+<p>The Carpentries Workshops and Instruction Team will provide
 Instructors with connection information for AMI instances the day before
 the workshop. Enough instances will be provided for each learner, and if
 requested, for each workshop helper, to have their own individual
@@ -469,8 +469,8 @@ <h3 id="does-the-aws-image-location-matter-do-i-need-to-set-up-an-ami-in-a-diffe
   "url": "https://datacarpentry.github.io/genomics-workshop/instructor/faq.html",
   "identifier": "https://datacarpentry.github.io/genomics-workshop/instructor/faq.html",
   "dateCreated": "2015-06-03",
-  "dateModified": "2024-01-08",
-  "datePublished": "2024-07-09"
+  "dateModified": "2024-07-13",
+  "datePublished": "2024-07-13"
 }
 
   </script><script>
diff --git a/instructor/index.html b/instructor/index.html
index fc41259f..ca8879cd 100644
--- a/instructor/index.html
+++ b/instructor/index.html
@@ -398,7 +398,7 @@ <h3 class="accordion-header" id="headingSpoiler1">
   Windows
   </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">
 <ul><li>Visit <a href="https://www.libreoffice.org/download/libreoffice-fresh/" class="external-link">the
 LibreOffice installation page</a>. The version for Windows should
@@ -478,7 +478,7 @@ <h3 class="accordion-header" id="headingSpoiler2">
   Mac OS X
   </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">
 <ul><li>Visit <a href="https://www.libreoffice.org/download/libreoffice-fresh/" class="external-link">the
 LibreOffice installation page</a>. The version for Mac should
@@ -500,7 +500,7 @@ <h3 class="accordion-header" id="headingSpoiler3">
   Linux
   </h3>
 </button>
-<div id="collapseSpoiler3" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler3" aria-labelledby="headingSpoiler3">
+<div id="collapseSpoiler3" class="accordion-collapse collapse" aria-labelledby="headingSpoiler3" data-bs-parent="#accordionSpoiler3">
 <div class="accordion-body">
 <ul><li>Visit <a href="https://www.libreoffice.org/download/libreoffice-fresh/" class="external-link">the
 LibreOffice installation page</a>. The version for Linux should
@@ -620,7 +620,7 @@ <h3 class="accordion-header" id="headingSpoiler4">
   Linux
   </h3>
 </button>
-<div id="collapseSpoiler4" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler4" aria-labelledby="headingSpoiler4">
+<div id="collapseSpoiler4" class="accordion-collapse collapse" aria-labelledby="headingSpoiler4" data-bs-parent="#accordionSpoiler4">
 <div class="accordion-body">
 <p>To install Conda, type:</p>
 <div class="codewrapper sourceCode" id="cb1">
@@ -643,7 +643,7 @@ <h3 class="accordion-header" id="headingSpoiler5">
   MacOS
   </h3>
 </button>
-<div id="collapseSpoiler5" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler5" aria-labelledby="headingSpoiler5">
+<div id="collapseSpoiler5" class="accordion-collapse collapse" aria-labelledby="headingSpoiler5" data-bs-parent="#accordionSpoiler5">
 <div class="accordion-body">
 <p>To install Conda, type:</p>
 <div class="codewrapper sourceCode" id="cb2">
@@ -669,7 +669,7 @@ <h3 class="accordion-header" id="headingSpoiler6">
   MacOS
   </h3>
 </button>
-<div id="collapseSpoiler6" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler6" aria-labelledby="headingSpoiler6">
+<div id="collapseSpoiler6" class="accordion-collapse collapse" aria-labelledby="headingSpoiler6" data-bs-parent="#accordionSpoiler6">
 <div class="accordion-body">
 <p>To install FastQC, type:</p>
 <div class="codewrapper sourceCode" id="cb3">
@@ -689,7 +689,7 @@ <h3 class="accordion-header" id="headingSpoiler7">
   FastQC Source Code Installation
   </h3>
 </button>
-<div id="collapseSpoiler7" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler7" aria-labelledby="headingSpoiler7">
+<div id="collapseSpoiler7" class="accordion-collapse collapse" aria-labelledby="headingSpoiler7" data-bs-parent="#accordionSpoiler7">
 <div class="accordion-body">
 <p>If you prefer to install from source, follow the directions
 below:</p>
@@ -735,7 +735,7 @@ <h3 class="accordion-header" id="headingSpoiler8">
   MacOS
   </h3>
 </button>
-<div id="collapseSpoiler8" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler8" aria-labelledby="headingSpoiler8">
+<div id="collapseSpoiler8" class="accordion-collapse collapse" aria-labelledby="headingSpoiler8" data-bs-parent="#accordionSpoiler8">
 <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>
@@ -754,7 +754,7 @@ <h3 class="accordion-header" id="headingSpoiler9">
   Trimmomatic Source Code Installation
   </h3>
 </button>
-<div id="collapseSpoiler9" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler9" aria-labelledby="headingSpoiler9">
+<div id="collapseSpoiler9" class="accordion-collapse collapse" aria-labelledby="headingSpoiler9" data-bs-parent="#accordionSpoiler9">
 <div class="accordion-body">
 <p>If you prefer to install from source, follow the directions
 below:</p>
@@ -793,7 +793,7 @@ <h3 class="accordion-header" id="headingSpoiler10">
   Simplify the Invocation, or to Test your installation if you installed with miniconda3:
   </h3>
 </button>
-<div id="collapseSpoiler10" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler10" aria-labelledby="headingSpoiler10">
+<div id="collapseSpoiler10" class="accordion-collapse collapse" aria-labelledby="headingSpoiler10" data-bs-parent="#accordionSpoiler10">
 <div class="accordion-body">
 <p>To simplify the invocation you could also create a script in the
 ~/bin folder:</p>
@@ -825,7 +825,7 @@ <h3 class="accordion-header" id="headingSpoiler11">
   MacOS
   </h3>
 </button>
-<div id="collapseSpoiler11" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler11" aria-labelledby="headingSpoiler11">
+<div id="collapseSpoiler11" class="accordion-collapse collapse" aria-labelledby="headingSpoiler11" data-bs-parent="#accordionSpoiler11">
 <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>
@@ -844,7 +844,7 @@ <h3 class="accordion-header" id="headingSpoiler12">
   BWA Source Code Installation
   </h3>
 </button>
-<div id="collapseSpoiler12" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler12" aria-labelledby="headingSpoiler12">
+<div id="collapseSpoiler12" class="accordion-collapse collapse" aria-labelledby="headingSpoiler12" data-bs-parent="#accordionSpoiler12">
 <div class="accordion-body">
 <p>If you prefer to install from source, follow the instructions
 below:</p>
@@ -879,7 +879,7 @@ <h3 class="accordion-header" id="headingSpoiler13">
   MacOS
   </h3>
 </button>
-<div id="collapseSpoiler13" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler13" aria-labelledby="headingSpoiler13">
+<div id="collapseSpoiler13" class="accordion-collapse collapse" aria-labelledby="headingSpoiler13" data-bs-parent="#accordionSpoiler13">
 <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>
@@ -914,7 +914,7 @@ <h3 class="accordion-header" id="headingSpoiler14">
   SAMtools Source Code Installation
   </h3>
 </button>
-<div id="collapseSpoiler14" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler14" aria-labelledby="headingSpoiler14">
+<div id="collapseSpoiler14" class="accordion-collapse collapse" aria-labelledby="headingSpoiler14" data-bs-parent="#accordionSpoiler14">
 <div class="accordion-body">
 <p>If you prefer to install from source, follow the instructions
 below:</p>
@@ -955,7 +955,7 @@ <h3 class="accordion-header" id="headingSpoiler15">
   MacOS
   </h3>
 </button>
-<div id="collapseSpoiler15" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler15" aria-labelledby="headingSpoiler15">
+<div id="collapseSpoiler15" class="accordion-collapse collapse" aria-labelledby="headingSpoiler15" data-bs-parent="#accordionSpoiler15">
 <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>
@@ -974,7 +974,7 @@ <h3 class="accordion-header" id="headingSpoiler16">
   BCF tools Source Code Installation
   </h3>
 </button>
-<div id="collapseSpoiler16" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler16" aria-labelledby="headingSpoiler16">
+<div id="collapseSpoiler16" class="accordion-collapse collapse" aria-labelledby="headingSpoiler16" data-bs-parent="#accordionSpoiler16">
 <div class="accordion-body">
 <p>If you prefer to install from source, follow the instructions
 below:</p>
@@ -1058,8 +1058,8 @@ <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": "2024-07-09",
-  "datePublished": "2024-07-09"
+  "dateModified": "2024-07-13",
+  "datePublished": "2024-07-13"
 }
 
   </script><script>
diff --git a/instructor/instructor-notes.html b/instructor/instructor-notes.html
index aca38597..76fb09cd 100644
--- a/instructor/instructor-notes.html
+++ b/instructor/instructor-notes.html
@@ -294,8 +294,8 @@ <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": "2024-07-09",
-  "datePublished": "2024-07-09"
+  "dateModified": "2024-07-13",
+  "datePublished": "2024-07-13"
 }
 
   </script><script>
diff --git a/instructor/profiles.html b/instructor/profiles.html
index 73c0d71b..85022def 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": "2024-07-09",
-  "datePublished": "2024-07-09"
+  "dateModified": "2024-07-13",
+  "datePublished": "2024-07-13"
 }
 
   </script><script>
diff --git a/instructor/reference.html b/instructor/reference.html
index 2bd60781..2d3e0c5f 100644
--- a/instructor/reference.html
+++ b/instructor/reference.html
@@ -289,7 +289,7 @@ <h1>Glossary</h1>
   "identifier": "https://datacarpentry.github.io/genomics-workshop/instructor/reference.html",
   "dateCreated": "2015-06-03",
   "dateModified": "2023-09-19",
-  "datePublished": "2024-07-09"
+  "datePublished": "2024-07-13"
 }
 
   </script><script>
diff --git a/instructor/teaching_demos.html b/instructor/teaching_demos.html
index 79e27c3b..42f99d58 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": "2024-07-09"
+  "datePublished": "2024-07-13"
 }
 
   </script><script>
diff --git a/md5sum.txt b/md5sum.txt
index bd33b926..3e266c90 100644
--- a/md5sum.txt
+++ b/md5sum.txt
@@ -4,7 +4,7 @@
 "config.yaml" "e0f88b2fa9a955366790c7554c781b0d" "site/built/config.yaml" "2023-09-19"
 "index.md" "06880077b0103010b1b550091f0f0936" "site/built/index.md" "2024-01-08"
 "instructors/AMI-setup.md" "64ecb146cd91d020872034b88ed145b7" "site/built/AMI-setup.md" "2023-09-19"
-"instructors/faq.md" "fb685c501943b1679eff3f491651824d" "site/built/faq.md" "2024-01-08"
+"instructors/faq.md" "9ae1f266942f3ff15d36219405bf35b4" "site/built/faq.md" "2024-07-13"
 "instructors/instructor-notes.md" "b963ac0859abcde3d03bb7c14fa38f69" "site/built/instructor-notes.md" "2023-09-19"
 "instructors/teaching_demos.md" "473ee41718bdc0fa0650372444851365" "site/built/teaching_demos.md" "2023-10-02"
 "learners/reference.md" "28853696c21dd22dfb883e9c241e95fb" "site/built/reference.md" "2023-09-19"
diff --git a/pkgdown.yml b/pkgdown.yml
index b1e6916c..b7198b43 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,4 +2,4 @@ pandoc: 3.1.11
 pkgdown: 2.1.0
 pkgdown_sha: ~
 articles: {}
-last_built: 2024-07-09T00:18Z
+last_built: 2024-07-13T15:35Z
diff --git a/profiles.html b/profiles.html
index 17f6a169..9a728af6 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": "2024-07-09",
-  "datePublished": "2024-07-09"
+  "dateModified": "2024-07-13",
+  "datePublished": "2024-07-13"
 }
 
   </script><script>
diff --git a/reference.html b/reference.html
index 9718f053..31068ab2 100644
--- a/reference.html
+++ b/reference.html
@@ -293,7 +293,7 @@ <h1>Glossary</h1>
   "identifier": "https://datacarpentry.github.io/genomics-workshop/reference.html",
   "dateCreated": "2015-06-03",
   "dateModified": "2023-09-19",
-  "datePublished": "2024-07-09"
+  "datePublished": "2024-07-13"
 }
 
   </script><script>
diff --git a/teaching_demos.html b/teaching_demos.html
index f3b604ab..5d41e824 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": "2024-07-09"
+  "datePublished": "2024-07-13"
 }
 
   </script><script>