From fb34e2b165b52b457a2511928da762018e23c4cc Mon Sep 17 00:00:00 2001
From: GitHub Actions <actions@github.com>
Date: Tue, 3 Sep 2024 00:26:42 +0000
Subject: [PATCH] site deploy

Auto-generated via {sandpaper}
Source  : eaade5b98c357753e34d6a1be673b95a91869b4e
Branch  : md-outputs
Author  : GitHub Actions <actions@github.com>
Time    : 2024-04-17 09:03:43 +0000
Message : markdown source builds

Auto-generated via {sandpaper}
Source  : 47a6ca444c3a4a04070da427b4f73d57d57bff3c
Branch  : main
Author  : vhmcck <114887733+vhmcck@users.noreply.github.com>
Time    : 2024-04-17 09:02:26 +0000
Message : Merge pull request #355 from datacarpentry/fix/permissions-example

Fix file permission flags in example
---
 01-introduction.html                  |  2 +-
 02-the-filesystem.html                |  2 +-
 03-working-with-files.html            | 14 +++++++-------
 04-redirection.html                   |  2 +-
 05-writing-scripts.html               |  2 +-
 06-organization.html                  |  2 +-
 404.html                              |  4 ++--
 CODE_OF_CONDUCT.html                  |  2 +-
 Extra_lesson.html                     |  2 +-
 LICENSE.html                          |  2 +-
 aio.html                              | 16 ++++++++--------
 discuss.html                          |  2 +-
 etherpad_template.html                |  2 +-
 images.html                           |  4 ++--
 index.html                            |  4 ++--
 instructor-notes.html                 |  4 ++--
 instructor/01-introduction.html       |  2 +-
 instructor/02-the-filesystem.html     |  2 +-
 instructor/03-working-with-files.html | 14 +++++++-------
 instructor/04-redirection.html        |  2 +-
 instructor/05-writing-scripts.html    |  2 +-
 instructor/06-organization.html       |  2 +-
 instructor/404.html                   |  4 ++--
 instructor/CODE_OF_CONDUCT.html       |  2 +-
 instructor/Extra_lesson.html          |  2 +-
 instructor/LICENSE.html               |  2 +-
 instructor/aio.html                   | 16 ++++++++--------
 instructor/discuss.html               |  2 +-
 instructor/etherpad_template.html     |  2 +-
 instructor/images.html                |  4 ++--
 instructor/index.html                 |  4 ++--
 instructor/instructor-notes.html      |  4 ++--
 instructor/key-points.html            |  4 ++--
 instructor/profiles.html              |  4 ++--
 instructor/reference.html             |  2 +-
 key-points.html                       |  4 ++--
 pkgdown.yml                           |  2 +-
 profiles.html                         |  4 ++--
 reference.html                        |  2 +-
 39 files changed, 77 insertions(+), 77 deletions(-)

diff --git a/01-introduction.html b/01-introduction.html
index 486bb93c..f1f0b72a 100644
--- a/01-introduction.html
+++ b/01-introduction.html
@@ -821,7 +821,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://datacarpentry.github.io/shell-genomics/01-introduction.html",
   "dateCreated": "2015-03-24",
   "dateModified": "2023-08-15",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/02-the-filesystem.html b/02-the-filesystem.html
index f88c7014..50b81a62 100644
--- a/02-the-filesystem.html
+++ b/02-the-filesystem.html
@@ -793,7 +793,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://datacarpentry.github.io/shell-genomics/02-the-filesystem.html",
   "dateCreated": "2015-03-24",
   "dateModified": "2023-05-08",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/03-working-with-files.html b/03-working-with-files.html
index 6968ced1..700c4844 100644
--- a/03-working-with-files.html
+++ b/03-working-with-files.html
@@ -448,7 +448,7 @@ <h3 class="callout-title">Exercise</h3>
 <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">
 <ol style="list-style-type: decimal"><li><code>ls /usr/bin/c*</code></li>
 <li><code>ls /usr/bin/*a*</code></li>
@@ -497,7 +497,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <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="cb10">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -584,7 +584,7 @@ <h3 class="callout-title">Exercise</h3>
 <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>First type <code>history</code>. Then use <code>!</code> followed by
 the line number to rerun that command.</p>
@@ -628,7 +628,7 @@ <h3 class="callout-title">Exercise</h3>
 <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">
 <ol style="list-style-type: decimal"><li>The last line of the file is
 <code>C:CCC::CCCCCCCC&lt;8?6A:C28C&lt;608'&amp;&amp;&amp;,'$</code>.</li>
@@ -698,7 +698,7 @@ <h3 class="callout-title">Exercise</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
   <h4 class="accordion-header" id="headingSolution5"> Show me the solution </h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
 <div class="accordion-body">
 <p><code>CAC</code></p>
 </div>
@@ -1044,7 +1044,7 @@ <h3 class="callout-title">Exercise</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution6" aria-expanded="false" aria-controls="collapseSolution6">
   <h4 class="accordion-header" id="headingSolution6"> Show me the solution </h4>
 </button>
-<div id="collapseSolution6" class="accordion-collapse collapse" aria-labelledby="headingSolution6" data-bs-parent="#accordionSolution6">
+<div id="collapseSolution6" class="accordion-collapse collapse" data-bs-parent="#accordionSolution6" aria-labelledby="headingSolution6">
 <div class="accordion-body">
 <ol style="list-style-type: decimal"><li><code>rm -r backup</code></li>
 <li>
@@ -1148,7 +1148,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://datacarpentry.github.io/shell-genomics/03-working-with-files.html",
   "dateCreated": "2015-03-24",
   "dateModified": "2023-05-08",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/04-redirection.html b/04-redirection.html
index f07337a8..5cccf2ae 100644
--- a/04-redirection.html
+++ b/04-redirection.html
@@ -1217,7 +1217,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://datacarpentry.github.io/shell-genomics/04-redirection.html",
   "dateCreated": "2015-03-24",
   "dateModified": "2024-03-14",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/05-writing-scripts.html b/05-writing-scripts.html
index f3e8a25f..3dfede5e 100644
--- a/05-writing-scripts.html
+++ b/05-writing-scripts.html
@@ -940,7 +940,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://datacarpentry.github.io/shell-genomics/05-writing-scripts.html",
   "dateCreated": "2015-03-24",
   "dateModified": "2024-04-17",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/06-organization.html b/06-organization.html
index 812862e5..3f730262 100644
--- a/06-organization.html
+++ b/06-organization.html
@@ -766,7 +766,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://datacarpentry.github.io/shell-genomics/06-organization.html",
   "dateCreated": "2015-03-24",
   "dateModified": "2023-05-08",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/404.html b/404.html
index 8844a93d..65af1b8c 100644
--- a/404.html
+++ b/404.html
@@ -364,8 +364,8 @@ <h1>Page not found</h1>
   "url": "https://datacarpentry.github.io/shell-genomics/404.html",
   "identifier": "https://datacarpentry.github.io/shell-genomics/404.html",
   "dateCreated": "2015-03-24",
-  "dateModified": "2024-08-27",
-  "datePublished": "2024-08-27"
+  "dateModified": "2024-09-03",
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html
index 794a028f..8b5772c6 100644
--- a/CODE_OF_CONDUCT.html
+++ b/CODE_OF_CONDUCT.html
@@ -385,7 +385,7 @@ <h1>Contributor Code of Conduct</h1>
   "identifier": "https://datacarpentry.github.io/shell-genomics/CODE_OF_CONDUCT.html",
   "dateCreated": "2015-03-24",
   "dateModified": "2023-05-08",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/Extra_lesson.html b/Extra_lesson.html
index 614ad227..da39bf55 100644
--- a/Extra_lesson.html
+++ b/Extra_lesson.html
@@ -761,7 +761,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
   "identifier": "https://datacarpentry.github.io/shell-genomics/Extra_lesson.html",
   "dateCreated": "2015-03-24",
   "dateModified": "2023-05-08",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/LICENSE.html b/LICENSE.html
index 2f79210f..8ac53658 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -433,7 +433,7 @@ <h1>Licenses</h1>
   "identifier": "https://datacarpentry.github.io/shell-genomics/LICENSE.html",
   "dateCreated": "2015-03-24",
   "dateModified": "2023-05-08",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/aio.html b/aio.html
index 39ba61b3..4d3b2333 100644
--- a/aio.html
+++ b/aio.html
@@ -1380,7 +1380,7 @@ <h3 class="callout-title">Exercise</h3>
 <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">
 <ol style="list-style-type: decimal">
 <li><code>ls /usr/bin/c*</code></li>
@@ -1431,7 +1431,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <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="cb10">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1522,7 +1522,7 @@ <h3 class="callout-title">Exercise</h3>
 <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>First type <code>history</code>. Then use <code>!</code> followed by
 the line number to rerun that command.</p>
@@ -1570,7 +1570,7 @@ <h3 class="callout-title">Exercise</h3>
 <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">
 <ol style="list-style-type: decimal">
 <li>The last line of the file is
@@ -1662,7 +1662,7 @@ <h3 class="callout-title">Exercise</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
   <h4 class="accordion-header" id="headingSolution5"> Show me the solution </h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
 <div class="accordion-body">
 <p><code>CAC</code></p>
 </div>
@@ -2037,7 +2037,7 @@ <h3 class="callout-title">Exercise</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution6" aria-expanded="false" aria-controls="collapseSolution6">
   <h4 class="accordion-header" id="headingSolution6"> Show me the solution </h4>
 </button>
-<div id="collapseSolution6" class="accordion-collapse collapse" aria-labelledby="headingSolution6" data-bs-parent="#accordionSolution6">
+<div id="collapseSolution6" class="accordion-collapse collapse" data-bs-parent="#accordionSolution6" aria-labelledby="headingSolution6">
 <div class="accordion-body">
 <ol style="list-style-type: decimal">
 <li><code>rm -r backup</code></li>
@@ -4003,8 +4003,8 @@ <h3 class="callout-title">Key Points</h3>
   "url": "https://datacarpentry.github.io/shell-genomics/aio.html",
   "identifier": "https://datacarpentry.github.io/shell-genomics/aio.html",
   "dateCreated": "2015-03-24",
-  "dateModified": "2024-08-27",
-  "datePublished": "2024-08-27"
+  "dateModified": "2024-09-03",
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/discuss.html b/discuss.html
index 0a75e823..803d3583 100644
--- a/discuss.html
+++ b/discuss.html
@@ -378,7 +378,7 @@ <h1>Discussion</h1>
   "identifier": "https://datacarpentry.github.io/shell-genomics/discuss.html",
   "dateCreated": "2015-03-24",
   "dateModified": "2023-05-08",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/etherpad_template.html b/etherpad_template.html
index 5080d9bb..4cc8226a 100644
--- a/etherpad_template.html
+++ b/etherpad_template.html
@@ -474,7 +474,7 @@ <h4 id="please-list-another-thing-you-found-less-useful-or-that-could-be-improve
   "identifier": "https://datacarpentry.github.io/shell-genomics/etherpad_template.html",
   "dateCreated": "2015-03-24",
   "dateModified": "2024-03-14",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/images.html b/images.html
index 11ef16f7..cc81c051 100644
--- a/images.html
+++ b/images.html
@@ -422,8 +422,8 @@ <h3 id="05-writing-scripts-figure-1">Figure 1</h3>
   "url": "https://datacarpentry.github.io/shell-genomics/images.html",
   "identifier": "https://datacarpentry.github.io/shell-genomics/images.html",
   "dateCreated": "2015-03-24",
-  "dateModified": "2024-08-27",
-  "datePublished": "2024-08-27"
+  "dateModified": "2024-09-03",
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/index.html b/index.html
index 554a4021..dcbb3866 100644
--- a/index.html
+++ b/index.html
@@ -411,8 +411,8 @@ <h3 class="callout-title">For Instructors</h3>
   "url": "https://datacarpentry.github.io/shell-genomics/index.html",
   "identifier": "https://datacarpentry.github.io/shell-genomics/index.html",
   "dateCreated": "2015-03-24",
-  "dateModified": "2024-08-27",
-  "datePublished": "2024-08-27"
+  "dateModified": "2024-09-03",
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor-notes.html b/instructor-notes.html
index 5275482a..f842ff22 100644
--- a/instructor-notes.html
+++ b/instructor-notes.html
@@ -500,8 +500,8 @@ <h4 id="command-prompt-editing">Command Prompt Editing<a class="anchor" aria-lab
   "url": "https://datacarpentry.github.io/shell-genomics/instructor-notes.html",
   "identifier": "https://datacarpentry.github.io/shell-genomics/instructor-notes.html",
   "dateCreated": "2015-03-24",
-  "dateModified": "2024-08-27",
-  "datePublished": "2024-08-27"
+  "dateModified": "2024-09-03",
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/01-introduction.html b/instructor/01-introduction.html
index c45fc166..fabacacb 100644
--- a/instructor/01-introduction.html
+++ b/instructor/01-introduction.html
@@ -823,7 +823,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://datacarpentry.github.io/shell-genomics/instructor/01-introduction.html",
   "dateCreated": "2015-03-24",
   "dateModified": "2023-08-15",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/02-the-filesystem.html b/instructor/02-the-filesystem.html
index 4c958597..de4e6917 100644
--- a/instructor/02-the-filesystem.html
+++ b/instructor/02-the-filesystem.html
@@ -795,7 +795,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://datacarpentry.github.io/shell-genomics/instructor/02-the-filesystem.html",
   "dateCreated": "2015-03-24",
   "dateModified": "2023-05-08",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/03-working-with-files.html b/instructor/03-working-with-files.html
index 671df033..304d0a4a 100644
--- a/instructor/03-working-with-files.html
+++ b/instructor/03-working-with-files.html
@@ -450,7 +450,7 @@ <h3 class="callout-title">Exercise</h3>
 <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">
 <ol style="list-style-type: decimal"><li><code>ls /usr/bin/c*</code></li>
 <li><code>ls /usr/bin/*a*</code></li>
@@ -499,7 +499,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <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="cb10">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -586,7 +586,7 @@ <h3 class="callout-title">Exercise</h3>
 <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>First type <code>history</code>. Then use <code>!</code> followed by
 the line number to rerun that command.</p>
@@ -630,7 +630,7 @@ <h3 class="callout-title">Exercise</h3>
 <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">
 <ol style="list-style-type: decimal"><li>The last line of the file is
 <code>C:CCC::CCCCCCCC&lt;8?6A:C28C&lt;608'&amp;&amp;&amp;,'$</code>.</li>
@@ -700,7 +700,7 @@ <h3 class="callout-title">Exercise</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
   <h4 class="accordion-header" id="headingSolution5"> Show me the solution </h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
 <div class="accordion-body">
 <p><code>CAC</code></p>
 </div>
@@ -1046,7 +1046,7 @@ <h3 class="callout-title">Exercise</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution6" aria-expanded="false" aria-controls="collapseSolution6">
   <h4 class="accordion-header" id="headingSolution6"> Show me the solution </h4>
 </button>
-<div id="collapseSolution6" class="accordion-collapse collapse" aria-labelledby="headingSolution6" data-bs-parent="#accordionSolution6">
+<div id="collapseSolution6" class="accordion-collapse collapse" data-bs-parent="#accordionSolution6" aria-labelledby="headingSolution6">
 <div class="accordion-body">
 <ol style="list-style-type: decimal"><li><code>rm -r backup</code></li>
 <li>
@@ -1150,7 +1150,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://datacarpentry.github.io/shell-genomics/instructor/03-working-with-files.html",
   "dateCreated": "2015-03-24",
   "dateModified": "2023-05-08",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/04-redirection.html b/instructor/04-redirection.html
index 13c50735..567e4a6f 100644
--- a/instructor/04-redirection.html
+++ b/instructor/04-redirection.html
@@ -1219,7 +1219,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://datacarpentry.github.io/shell-genomics/instructor/04-redirection.html",
   "dateCreated": "2015-03-24",
   "dateModified": "2024-03-14",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/05-writing-scripts.html b/instructor/05-writing-scripts.html
index 66a3c96e..4aa4dbcb 100644
--- a/instructor/05-writing-scripts.html
+++ b/instructor/05-writing-scripts.html
@@ -942,7 +942,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://datacarpentry.github.io/shell-genomics/instructor/05-writing-scripts.html",
   "dateCreated": "2015-03-24",
   "dateModified": "2024-04-17",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/06-organization.html b/instructor/06-organization.html
index 1e7e30d6..334b5504 100644
--- a/instructor/06-organization.html
+++ b/instructor/06-organization.html
@@ -768,7 +768,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://datacarpentry.github.io/shell-genomics/instructor/06-organization.html",
   "dateCreated": "2015-03-24",
   "dateModified": "2023-05-08",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/404.html b/instructor/404.html
index 0d27d424..6bb38b60 100644
--- a/instructor/404.html
+++ b/instructor/404.html
@@ -364,8 +364,8 @@ <h1>Page not found</h1>
   "url": "https://datacarpentry.github.io/shell-genomics/instructor/404.html",
   "identifier": "https://datacarpentry.github.io/shell-genomics/instructor/404.html",
   "dateCreated": "2015-03-24",
-  "dateModified": "2024-08-27",
-  "datePublished": "2024-08-27"
+  "dateModified": "2024-09-03",
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/CODE_OF_CONDUCT.html b/instructor/CODE_OF_CONDUCT.html
index 1059077b..696b1e93 100644
--- a/instructor/CODE_OF_CONDUCT.html
+++ b/instructor/CODE_OF_CONDUCT.html
@@ -387,7 +387,7 @@ <h1>Contributor Code of Conduct</h1>
   "identifier": "https://datacarpentry.github.io/shell-genomics/instructor/CODE_OF_CONDUCT.html",
   "dateCreated": "2015-03-24",
   "dateModified": "2023-05-08",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/Extra_lesson.html b/instructor/Extra_lesson.html
index cf29582f..c7ac759c 100644
--- a/instructor/Extra_lesson.html
+++ b/instructor/Extra_lesson.html
@@ -763,7 +763,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
   "identifier": "https://datacarpentry.github.io/shell-genomics/instructor/Extra_lesson.html",
   "dateCreated": "2015-03-24",
   "dateModified": "2023-05-08",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/LICENSE.html b/instructor/LICENSE.html
index c38c50ef..cb1c5b40 100644
--- a/instructor/LICENSE.html
+++ b/instructor/LICENSE.html
@@ -435,7 +435,7 @@ <h1>Licenses</h1>
   "identifier": "https://datacarpentry.github.io/shell-genomics/instructor/LICENSE.html",
   "dateCreated": "2015-03-24",
   "dateModified": "2023-05-08",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/aio.html b/instructor/aio.html
index 208f6dcc..5cf4ee2f 100644
--- a/instructor/aio.html
+++ b/instructor/aio.html
@@ -1389,7 +1389,7 @@ <h3 class="callout-title">Exercise</h3>
 <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">
 <ol style="list-style-type: decimal">
 <li><code>ls /usr/bin/c*</code></li>
@@ -1440,7 +1440,7 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 <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="cb10">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1531,7 +1531,7 @@ <h3 class="callout-title">Exercise</h3>
 <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>First type <code>history</code>. Then use <code>!</code> followed by
 the line number to rerun that command.</p>
@@ -1579,7 +1579,7 @@ <h3 class="callout-title">Exercise</h3>
 <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">
 <ol style="list-style-type: decimal">
 <li>The last line of the file is
@@ -1671,7 +1671,7 @@ <h3 class="callout-title">Exercise</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
   <h4 class="accordion-header" id="headingSolution5"> Show me the solution </h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
 <div class="accordion-body">
 <p><code>CAC</code></p>
 </div>
@@ -2046,7 +2046,7 @@ <h3 class="callout-title">Exercise</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution6" aria-expanded="false" aria-controls="collapseSolution6">
   <h4 class="accordion-header" id="headingSolution6"> Show me the solution </h4>
 </button>
-<div id="collapseSolution6" class="accordion-collapse collapse" aria-labelledby="headingSolution6" data-bs-parent="#accordionSolution6">
+<div id="collapseSolution6" class="accordion-collapse collapse" data-bs-parent="#accordionSolution6" aria-labelledby="headingSolution6">
 <div class="accordion-body">
 <ol style="list-style-type: decimal">
 <li><code>rm -r backup</code></li>
@@ -4015,8 +4015,8 @@ <h3 class="callout-title">Key Points</h3>
   "url": "https://datacarpentry.github.io/shell-genomics/instructor/aio.html",
   "identifier": "https://datacarpentry.github.io/shell-genomics/instructor/aio.html",
   "dateCreated": "2015-03-24",
-  "dateModified": "2024-08-27",
-  "datePublished": "2024-08-27"
+  "dateModified": "2024-09-03",
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/discuss.html b/instructor/discuss.html
index b3b1b9f0..7d614102 100644
--- a/instructor/discuss.html
+++ b/instructor/discuss.html
@@ -380,7 +380,7 @@ <h1>Discussion</h1>
   "identifier": "https://datacarpentry.github.io/shell-genomics/instructor/discuss.html",
   "dateCreated": "2015-03-24",
   "dateModified": "2023-05-08",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/etherpad_template.html b/instructor/etherpad_template.html
index 7030428e..aecfc4e4 100644
--- a/instructor/etherpad_template.html
+++ b/instructor/etherpad_template.html
@@ -476,7 +476,7 @@ <h4 id="please-list-another-thing-you-found-less-useful-or-that-could-be-improve
   "identifier": "https://datacarpentry.github.io/shell-genomics/instructor/etherpad_template.html",
   "dateCreated": "2015-03-24",
   "dateModified": "2024-03-14",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/images.html b/instructor/images.html
index f7b7d001..a22d0e96 100644
--- a/instructor/images.html
+++ b/instructor/images.html
@@ -428,8 +428,8 @@ <h3 id="05-writing-scripts-figure-1">Figure 1</h3>
   "url": "https://datacarpentry.github.io/shell-genomics/instructor/images.html",
   "identifier": "https://datacarpentry.github.io/shell-genomics/instructor/images.html",
   "dateCreated": "2015-03-24",
-  "dateModified": "2024-08-27",
-  "datePublished": "2024-08-27"
+  "dateModified": "2024-09-03",
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/index.html b/instructor/index.html
index fe7a58e6..d3da7aa4 100644
--- a/instructor/index.html
+++ b/instructor/index.html
@@ -489,8 +489,8 @@ <h3 class="callout-title">For Instructors</h3>
   "url": "https://datacarpentry.github.io/shell-genomics/instructor/index.html",
   "identifier": "https://datacarpentry.github.io/shell-genomics/instructor/index.html",
   "dateCreated": "2015-03-24",
-  "dateModified": "2024-08-27",
-  "datePublished": "2024-08-27"
+  "dateModified": "2024-09-03",
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/instructor-notes.html b/instructor/instructor-notes.html
index 78002d98..0e63e382 100644
--- a/instructor/instructor-notes.html
+++ b/instructor/instructor-notes.html
@@ -512,8 +512,8 @@ <h4 id="command-prompt-editing">Command Prompt Editing<a class="anchor" aria-lab
   "url": "https://datacarpentry.github.io/shell-genomics/instructor/instructor-notes.html",
   "identifier": "https://datacarpentry.github.io/shell-genomics/instructor/instructor-notes.html",
   "dateCreated": "2015-03-24",
-  "dateModified": "2024-08-27",
-  "datePublished": "2024-08-27"
+  "dateModified": "2024-09-03",
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/key-points.html b/instructor/key-points.html
index 9ade521e..e1e172f6 100644
--- a/instructor/key-points.html
+++ b/instructor/key-points.html
@@ -480,8 +480,8 @@ <h2 class="accordion-header" id="flush-headingTwelve">
   "url": "https://datacarpentry.github.io/shell-genomics/instructor/key-points.html",
   "identifier": "https://datacarpentry.github.io/shell-genomics/instructor/key-points.html",
   "dateCreated": "2015-03-24",
-  "dateModified": "2024-08-27",
-  "datePublished": "2024-08-27"
+  "dateModified": "2024-09-03",
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/profiles.html b/instructor/profiles.html
index 5f9432eb..8a6928ba 100644
--- a/instructor/profiles.html
+++ b/instructor/profiles.html
@@ -336,8 +336,8 @@ <h1>Learner Profiles</h1>
   "url": "https://datacarpentry.github.io/shell-genomics/instructor/profiles.html",
   "identifier": "https://datacarpentry.github.io/shell-genomics/instructor/profiles.html",
   "dateCreated": "2015-03-24",
-  "dateModified": "2024-08-27",
-  "datePublished": "2024-08-27"
+  "dateModified": "2024-09-03",
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/reference.html b/instructor/reference.html
index d558904c..9add3011 100644
--- a/instructor/reference.html
+++ b/instructor/reference.html
@@ -655,7 +655,7 @@ <h3 id="high-throughput-sequencing">High-throughput sequencing<a class="anchor"
   "identifier": "https://datacarpentry.github.io/shell-genomics/instructor/reference.html",
   "dateCreated": "2015-03-24",
   "dateModified": "2023-05-08",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/key-points.html b/key-points.html
index ad453ee0..debe026d 100644
--- a/key-points.html
+++ b/key-points.html
@@ -474,8 +474,8 @@ <h2 class="accordion-header" id="flush-headingTwelve">
   "url": "https://datacarpentry.github.io/shell-genomics/key-points.html",
   "identifier": "https://datacarpentry.github.io/shell-genomics/key-points.html",
   "dateCreated": "2015-03-24",
-  "dateModified": "2024-08-27",
-  "datePublished": "2024-08-27"
+  "dateModified": "2024-09-03",
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/pkgdown.yml b/pkgdown.yml
index 47a0024f..b746f2f1 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,4 +2,4 @@ pandoc: 3.1.11
 pkgdown: 2.1.0
 pkgdown_sha: ~
 articles: {}
-last_built: 2024-08-27T00:26Z
+last_built: 2024-09-03T00:26Z
diff --git a/profiles.html b/profiles.html
index 5d0d10f2..92feb093 100644
--- a/profiles.html
+++ b/profiles.html
@@ -336,8 +336,8 @@ <h1>Learner Profiles</h1>
   "url": "https://datacarpentry.github.io/shell-genomics/profiles.html",
   "identifier": "https://datacarpentry.github.io/shell-genomics/profiles.html",
   "dateCreated": "2015-03-24",
-  "dateModified": "2024-08-27",
-  "datePublished": "2024-08-27"
+  "dateModified": "2024-09-03",
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/reference.html b/reference.html
index fb06843a..03712abf 100644
--- a/reference.html
+++ b/reference.html
@@ -653,7 +653,7 @@ <h3 id="high-throughput-sequencing">High-throughput sequencing<a class="anchor"
   "identifier": "https://datacarpentry.github.io/shell-genomics/reference.html",
   "dateCreated": "2015-03-24",
   "dateModified": "2023-05-08",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>