From ff1c9cb4a61bba3d55e95fa98432149c1205a1de Mon Sep 17 00:00:00 2001
From: GitHub Actions <actions@github.com>
Date: Tue, 3 Sep 2024 00:56:46 +0000
Subject: [PATCH] site deploy

Auto-generated via {sandpaper}
Source  : 99a59a89c740eebc2097d8f1e9256a555fe83a4f
Branch  : md-outputs
Author  : GitHub Actions <actions@github.com>
Time    : 2024-03-11 14:09:18 +0000
Message : markdown source builds

Auto-generated via {sandpaper}
Source  : 83d5542ea901054de6f482aa7d00dc6610d30f3a
Branch  : main
Author  : Tim Booth <tim.booth@ed.ac.uk>
Time    : 2024-03-11 14:06:49 +0000
Message : Update of Sandpaper
---
 01-introduction.html                  |  2 +-
 02-placeholders.html                  |  2 +-
 03-chaining_rules.html                |  2 +-
 04-the_dag.html                       |  2 +-
 05-expansion.html                     |  2 +-
 06-awkward_programs.html              |  8 +++----
 07-finished-workflow.html             | 10 ++++-----
 08-configuring.html                   |  8 +++----
 09-performance.html                   |  2 +-
 10-conda_integration.html             |  6 ++---
 11-assembly_challenge.html            |  6 ++---
 12-cleaning_up.html                   |  2 +-
 13-quoting.html                       |  2 +-
 404.html                              |  4 ++--
 CODE_OF_CONDUCT.html                  |  2 +-
 LICENSE.html                          |  2 +-
 aio.html                              | 32 +++++++++++++--------------
 discuss.html                          |  2 +-
 images.html                           |  4 ++--
 index.html                            |  4 ++--
 instructor-notes.html                 |  4 ++--
 instructor/01-introduction.html       |  2 +-
 instructor/02-placeholders.html       |  2 +-
 instructor/03-chaining_rules.html     |  2 +-
 instructor/04-the_dag.html            |  2 +-
 instructor/05-expansion.html          |  2 +-
 instructor/06-awkward_programs.html   |  8 +++----
 instructor/07-finished-workflow.html  | 10 ++++-----
 instructor/08-configuring.html        |  8 +++----
 instructor/09-performance.html        |  2 +-
 instructor/10-conda_integration.html  |  6 ++---
 instructor/11-assembly_challenge.html |  6 ++---
 instructor/12-cleaning_up.html        |  2 +-
 instructor/13-quoting.html            |  2 +-
 instructor/404.html                   |  4 ++--
 instructor/CODE_OF_CONDUCT.html       |  2 +-
 instructor/LICENSE.html               |  2 +-
 instructor/aio.html                   | 32 +++++++++++++--------------
 instructor/discuss.html               |  2 +-
 instructor/images.html                |  4 ++--
 instructor/index.html                 |  4 ++--
 instructor/instructor-notes.html      |  4 ++--
 instructor/key-points.html            |  4 ++--
 instructor/paper.html                 |  2 +-
 instructor/profiles.html              |  4 ++--
 instructor/reference.html             |  2 +-
 key-points.html                       |  4 ++--
 paper.html                            |  2 +-
 pkgdown.yml                           |  2 +-
 profiles.html                         |  4 ++--
 reference.html                        |  2 +-
 51 files changed, 121 insertions(+), 121 deletions(-)

diff --git a/01-introduction.html b/01-introduction.html
index 6763ac5..592773b 100644
--- a/01-introduction.html
+++ b/01-introduction.html
@@ -748,7 +748,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/01-introduction.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-02-22",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/02-placeholders.html b/02-placeholders.html
index ce6a971..c933d5b 100644
--- a/02-placeholders.html
+++ b/02-placeholders.html
@@ -807,7 +807,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/02-placeholders.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-02-23",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/03-chaining_rules.html b/03-chaining_rules.html
index 4bc6f62..6afb9f9 100644
--- a/03-chaining_rules.html
+++ b/03-chaining_rules.html
@@ -932,7 +932,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/03-chaining_rules.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-03-01",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/04-the_dag.html b/04-the_dag.html
index 9d9af25..e21efb5 100644
--- a/04-the_dag.html
+++ b/04-the_dag.html
@@ -832,7 +832,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/04-the_dag.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-03-11",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/05-expansion.html b/05-expansion.html
index dd53eaa..11ba773 100644
--- a/05-expansion.html
+++ b/05-expansion.html
@@ -959,7 +959,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/05-expansion.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-02-23",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/06-awkward_programs.html b/06-awkward_programs.html
index f07724e..54bb3d9 100644
--- a/06-awkward_programs.html
+++ b/06-awkward_programs.html
@@ -530,7 +530,7 @@ <h3 class="callout-title">Adding a FastQC rule using the default output file nam
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>Since the <code>shell</code> command is not to be changed, the output
 names will be dictated by FastQC as we saw when running the command
@@ -586,7 +586,7 @@ <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" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <p>This involves using the {myfile} wildcard twice and then constructing
 the output directory name to place in the <code>-o</code> option to
@@ -718,7 +718,7 @@ <h3 class="callout-title">Fixing FastQC to use our own output file names</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" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <p>This is one solution, using <code>-o .</code> to tell FastQC to
 produce the files in the current directory, then explicitly renaming
@@ -860,7 +860,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/06-awkward_programs.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-03-01",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/07-finished-workflow.html b/07-finished-workflow.html
index 21ac5c3..94dcc9b 100644
--- a/07-finished-workflow.html
+++ b/07-finished-workflow.html
@@ -509,7 +509,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <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">
 <pre class="source"><code>rule salmon_quant:
     output: directory("salmon.{sample}")
@@ -576,7 +576,7 @@ <h3 class="callout-title">Adding a MultiQC rule</h3>
 <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">
 <pre class="source"><code>rule multiqc:
     output: directory('multiqc_out')
@@ -634,7 +634,7 @@ <h3 class="callout-title">Fixing Kallisto</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">
 <pre class="source"><code># Kallisto quantification of one sample, with log capture.
 rule kallisto_quant:
@@ -694,7 +694,7 @@ <h3 class="callout-title">Making the MultiQC rule more robust</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">
 <p>This solution will work with the version of <em>kallisto_quant</em>
 in the solution above.</p>
@@ -810,7 +810,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/07-finished-workflow.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-03-01",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/08-configuring.html b/08-configuring.html
index 59be7e4..0ec297c 100644
--- a/08-configuring.html
+++ b/08-configuring.html
@@ -474,7 +474,7 @@ <h3 class="callout-title">Adding a parameter to the
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <pre class="source"><code>rule salmon_index:
     output:
@@ -573,7 +573,7 @@ <h3 class="callout-title">Making the parameter of a rule configurable</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <p>Rule is as before, aside from:</p>
 <pre class="source"><code><span><span class="va">params</span><span class="op">:</span></span>
@@ -646,7 +646,7 @@ <h3 class="callout-title">Making the conditions and replicates into configurable
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <p>In <em>config.yaml</em> add the lines:</p>
 <pre class="source"><code>conditions: ["etoh60", "temp33", "ref"]
@@ -756,7 +756,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/08-configuring.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-03-11",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/09-performance.html b/09-performance.html
index 23f3c5a..362d896 100644
--- a/09-performance.html
+++ b/09-performance.html
@@ -730,7 +730,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/09-performance.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-03-01",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/10-conda_integration.html b/10-conda_integration.html
index 3ea0d7b..ea13b3a 100644
--- a/10-conda_integration.html
+++ b/10-conda_integration.html
@@ -535,7 +535,7 @@ <h3 class="callout-title">Queryting and installing Conda packages</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>There are several ways of doing this, but one using the commands
 above is:</li>
@@ -674,7 +674,7 @@ <h3 class="callout-title">Using an older version of Salmon</h3>
 <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">
 <p>The first thing that we need is an appropriate YAML file. It’s
 possible to write one from scratch in a text editor, but for this answer
@@ -827,7 +827,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/10-conda_integration.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-03-11",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/11-assembly_challenge.html b/11-assembly_challenge.html
index 1e2a403..9ba89fb 100644
--- a/11-assembly_challenge.html
+++ b/11-assembly_challenge.html
@@ -487,7 +487,7 @@ <h3 class="callout-title">Running the Bash script</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">
 <p>The commands to build and activate the Conda env can be found in the
 “Conda Integration” chapter.</p>
@@ -616,7 +616,7 @@ <h3 class="callout-title">Challenge - building a full Snakemake workflow</h3>
 <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">
 <p>A sample solution to this exercise <a href="files/assembly_with_conda.Snakefile">is available here</a>, along
 with a suitable <a href="files/assembly_conda_env.yaml">Conda
@@ -704,7 +704,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/11-assembly_challenge.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-03-01",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/12-cleaning_up.html b/12-cleaning_up.html
index 8681580..d5e18a1 100644
--- a/12-cleaning_up.html
+++ b/12-cleaning_up.html
@@ -785,7 +785,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/12-cleaning_up.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-03-11",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/13-quoting.html b/13-quoting.html
index ef525f1..eb883da 100644
--- a/13-quoting.html
+++ b/13-quoting.html
@@ -733,7 +733,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/13-quoting.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-03-01",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/404.html b/404.html
index 3a8760d..d9c8966 100644
--- a/404.html
+++ b/404.html
@@ -451,8 +451,8 @@ <h1>Page not found</h1>
   "url": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/404.html",
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/404.html",
   "dateCreated": "2021-03-26",
-  "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 4e39536..296e204 100644
--- a/CODE_OF_CONDUCT.html
+++ b/CODE_OF_CONDUCT.html
@@ -458,7 +458,7 @@ <h1>Contributor Code of Conduct</h1>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/CODE_OF_CONDUCT.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-02-22",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/LICENSE.html b/LICENSE.html
index a87e8b5..2736e4b 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -561,7 +561,7 @@ <h3 id="yeast-transcriptome">Yeast transcriptome<a class="anchor" aria-label="an
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/LICENSE.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-02-22",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/aio.html b/aio.html
index 473f000..bdb7b21 100644
--- a/aio.html
+++ b/aio.html
@@ -2730,7 +2730,7 @@ <h3 class="callout-title">Adding a FastQC rule using the default output file nam
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>Since the <code>shell</code> command is not to be changed, the output
 names will be dictated by FastQC as we saw when running the command
@@ -2787,7 +2787,7 @@ <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" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <p>This involves using the {myfile} wildcard twice and then constructing
 the output directory name to place in the <code>-o</code> option to
@@ -2921,7 +2921,7 @@ <h3 class="callout-title">Fixing FastQC to use our own output file names</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" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <p>This is one solution, using <code>-o .</code> to tell FastQC to
 produce the files in the current directory, then explicitly renaming
@@ -3134,7 +3134,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <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">
 <pre class="source"><code>rule salmon_quant:
     output: directory("salmon.{sample}")
@@ -3205,7 +3205,7 @@ <h3 class="callout-title">Adding a MultiQC rule</h3>
 <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">
 <pre class="source"><code>rule multiqc:
     output: directory('multiqc_out')
@@ -3265,7 +3265,7 @@ <h3 class="callout-title">Fixing Kallisto</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">
 <pre class="source"><code># Kallisto quantification of one sample, with log capture.
 rule kallisto_quant:
@@ -3327,7 +3327,7 @@ <h3 class="callout-title">Making the MultiQC rule more robust</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">
 <p>This solution will work with the version of <em>kallisto_quant</em>
 in the solution above.</p>
@@ -3472,7 +3472,7 @@ <h3 class="callout-title">Adding a parameter to the
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <pre class="source"><code>rule salmon_index:
     output:
@@ -3575,7 +3575,7 @@ <h3 class="callout-title">Making the parameter of a rule configurable</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <p>Rule is as before, aside from:</p>
 <pre class="source"><code><span><span class="va">params</span><span class="op">:</span></span>
@@ -3652,7 +3652,7 @@ <h3 class="callout-title">Making the conditions and replicates into configurable
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <p>In <em>config.yaml</em> add the lines:</p>
 <pre class="source"><code>conditions: ["etoh60", "temp33", "ref"]
@@ -4175,7 +4175,7 @@ <h3 class="callout-title">Queryting and installing Conda packages</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>There are several ways of doing this, but one using the commands
@@ -4320,7 +4320,7 @@ <h3 class="callout-title">Using an older version of Salmon</h3>
 <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">
 <p>The first thing that we need is an appropriate YAML file. It’s
 possible to write one from scratch in a text editor, but for this answer
@@ -4515,7 +4515,7 @@ <h3 class="callout-title">Running the Bash script</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">
 <p>The commands to build and activate the Conda env can be found in the
 “Conda Integration” chapter.</p>
@@ -4668,7 +4668,7 @@ <h3 class="callout-title">Challenge - building a full Snakemake workflow</h3>
 <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">
 <p>A sample solution to this exercise <a href="files/assembly_with_conda.Snakefile">is available here</a>, along
 with a suitable <a href="files/assembly_conda_env.yaml">Conda
@@ -5391,8 +5391,8 @@ <h3 class="callout-title">Key Points</h3>
   "url": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/aio.html",
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/aio.html",
   "dateCreated": "2021-03-26",
-  "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 4091272..05c3c80 100644
--- a/discuss.html
+++ b/discuss.html
@@ -452,7 +452,7 @@ <h1>Discussion</h1>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/discuss.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-02-22",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/images.html b/images.html
index 597240a..56ec627 100644
--- a/images.html
+++ b/images.html
@@ -537,8 +537,8 @@ <h3 id="11-assembly_challenge-figure-1">Figure 1</h3>
   "url": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/images.html",
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/images.html",
   "dateCreated": "2021-03-26",
-  "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 57b77d5..619b21b 100644
--- a/index.html
+++ b/index.html
@@ -620,8 +620,8 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
   "url": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/index.html",
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/index.html",
   "dateCreated": "2021-03-26",
-  "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 2407800..39c88d9 100644
--- a/instructor-notes.html
+++ b/instructor-notes.html
@@ -586,8 +586,8 @@ <h2 id="episode-03---chaining-rules">Episode 03 - Chaining rules<a class="anchor
   "url": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor-notes.html",
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor-notes.html",
   "dateCreated": "2021-03-26",
-  "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 05ecfa7..8deb853 100644
--- a/instructor/01-introduction.html
+++ b/instructor/01-introduction.html
@@ -750,7 +750,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/01-introduction.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-02-22",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/02-placeholders.html b/instructor/02-placeholders.html
index 3544538..d5651b9 100644
--- a/instructor/02-placeholders.html
+++ b/instructor/02-placeholders.html
@@ -809,7 +809,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/02-placeholders.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-02-23",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/03-chaining_rules.html b/instructor/03-chaining_rules.html
index bd4408b..5b28bf7 100644
--- a/instructor/03-chaining_rules.html
+++ b/instructor/03-chaining_rules.html
@@ -934,7 +934,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/03-chaining_rules.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-03-01",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/04-the_dag.html b/instructor/04-the_dag.html
index 39bf852..147b9f5 100644
--- a/instructor/04-the_dag.html
+++ b/instructor/04-the_dag.html
@@ -834,7 +834,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/04-the_dag.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-03-11",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/05-expansion.html b/instructor/05-expansion.html
index efb9cae..4be0021 100644
--- a/instructor/05-expansion.html
+++ b/instructor/05-expansion.html
@@ -961,7 +961,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/05-expansion.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-02-23",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/06-awkward_programs.html b/instructor/06-awkward_programs.html
index 2314037..d701630 100644
--- a/instructor/06-awkward_programs.html
+++ b/instructor/06-awkward_programs.html
@@ -532,7 +532,7 @@ <h3 class="callout-title">Adding a FastQC rule using the default output file nam
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>Since the <code>shell</code> command is not to be changed, the output
 names will be dictated by FastQC as we saw when running the command
@@ -588,7 +588,7 @@ <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" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <p>This involves using the {myfile} wildcard twice and then constructing
 the output directory name to place in the <code>-o</code> option to
@@ -720,7 +720,7 @@ <h3 class="callout-title">Fixing FastQC to use our own output file names</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" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <p>This is one solution, using <code>-o .</code> to tell FastQC to
 produce the files in the current directory, then explicitly renaming
@@ -862,7 +862,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/06-awkward_programs.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-03-01",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/07-finished-workflow.html b/instructor/07-finished-workflow.html
index 91fedea..5975591 100644
--- a/instructor/07-finished-workflow.html
+++ b/instructor/07-finished-workflow.html
@@ -511,7 +511,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <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">
 <pre class="source"><code>rule salmon_quant:
     output: directory("salmon.{sample}")
@@ -578,7 +578,7 @@ <h3 class="callout-title">Adding a MultiQC rule</h3>
 <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">
 <pre class="source"><code>rule multiqc:
     output: directory('multiqc_out')
@@ -636,7 +636,7 @@ <h3 class="callout-title">Fixing Kallisto</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">
 <pre class="source"><code># Kallisto quantification of one sample, with log capture.
 rule kallisto_quant:
@@ -696,7 +696,7 @@ <h3 class="callout-title">Making the MultiQC rule more robust</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">
 <p>This solution will work with the version of <em>kallisto_quant</em>
 in the solution above.</p>
@@ -812,7 +812,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/07-finished-workflow.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-03-01",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/08-configuring.html b/instructor/08-configuring.html
index 618418e..e332945 100644
--- a/instructor/08-configuring.html
+++ b/instructor/08-configuring.html
@@ -476,7 +476,7 @@ <h3 class="callout-title">Adding a parameter to the
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <pre class="source"><code>rule salmon_index:
     output:
@@ -575,7 +575,7 @@ <h3 class="callout-title">Making the parameter of a rule configurable</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <p>Rule is as before, aside from:</p>
 <pre class="source"><code><span><span class="va">params</span><span class="op">:</span></span>
@@ -648,7 +648,7 @@ <h3 class="callout-title">Making the conditions and replicates into configurable
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <p>In <em>config.yaml</em> add the lines:</p>
 <pre class="source"><code>conditions: ["etoh60", "temp33", "ref"]
@@ -758,7 +758,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/08-configuring.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-03-11",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/09-performance.html b/instructor/09-performance.html
index 58bc2e3..ac4a858 100644
--- a/instructor/09-performance.html
+++ b/instructor/09-performance.html
@@ -732,7 +732,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/09-performance.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-03-01",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/10-conda_integration.html b/instructor/10-conda_integration.html
index 16cf7ad..5f3a905 100644
--- a/instructor/10-conda_integration.html
+++ b/instructor/10-conda_integration.html
@@ -537,7 +537,7 @@ <h3 class="callout-title">Queryting and installing Conda packages</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>There are several ways of doing this, but one using the commands
 above is:</li>
@@ -676,7 +676,7 @@ <h3 class="callout-title">Using an older version of Salmon</h3>
 <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">
 <p>The first thing that we need is an appropriate YAML file. It’s
 possible to write one from scratch in a text editor, but for this answer
@@ -829,7 +829,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/10-conda_integration.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-03-11",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/11-assembly_challenge.html b/instructor/11-assembly_challenge.html
index a19d841..45ae32a 100644
--- a/instructor/11-assembly_challenge.html
+++ b/instructor/11-assembly_challenge.html
@@ -489,7 +489,7 @@ <h3 class="callout-title">Running the Bash script</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">
 <p>The commands to build and activate the Conda env can be found in the
 “Conda Integration” chapter.</p>
@@ -618,7 +618,7 @@ <h3 class="callout-title">Challenge - building a full Snakemake workflow</h3>
 <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">
 <p>A sample solution to this exercise <a href="../files/assembly_with_conda.Snakefile">is available here</a>, along
 with a suitable <a href="../files/assembly_conda_env.yaml">Conda
@@ -706,7 +706,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/11-assembly_challenge.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-03-01",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/12-cleaning_up.html b/instructor/12-cleaning_up.html
index 3002374..49aff9c 100644
--- a/instructor/12-cleaning_up.html
+++ b/instructor/12-cleaning_up.html
@@ -787,7 +787,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/12-cleaning_up.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-03-11",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/13-quoting.html b/instructor/13-quoting.html
index 1a95777..80308cd 100644
--- a/instructor/13-quoting.html
+++ b/instructor/13-quoting.html
@@ -735,7 +735,7 @@ <h3 class="callout-title">Key Points</h3>
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   "dateCreated": "2021-03-26",
   "dateModified": "2024-03-01",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/404.html b/instructor/404.html
index de7984e..fa423e8 100644
--- a/instructor/404.html
+++ b/instructor/404.html
@@ -451,8 +451,8 @@ <h1>Page not found</h1>
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   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/404.html",
   "dateCreated": "2021-03-26",
-  "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 e3bbd8a..245748c 100644
--- a/instructor/CODE_OF_CONDUCT.html
+++ b/instructor/CODE_OF_CONDUCT.html
@@ -460,7 +460,7 @@ <h1>Contributor Code of Conduct</h1>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/CODE_OF_CONDUCT.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-02-22",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/LICENSE.html b/instructor/LICENSE.html
index 461518d..6cb1ff4 100644
--- a/instructor/LICENSE.html
+++ b/instructor/LICENSE.html
@@ -563,7 +563,7 @@ <h3 id="yeast-transcriptome">Yeast transcriptome<a class="anchor" aria-label="an
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/LICENSE.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-02-22",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/aio.html b/instructor/aio.html
index b66281c..fb7e60e 100644
--- a/instructor/aio.html
+++ b/instructor/aio.html
@@ -2738,7 +2738,7 @@ <h3 class="callout-title">Adding a FastQC rule using the default output file nam
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <p>Since the <code>shell</code> command is not to be changed, the output
 names will be dictated by FastQC as we saw when running the command
@@ -2795,7 +2795,7 @@ <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" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <p>This involves using the {myfile} wildcard twice and then constructing
 the output directory name to place in the <code>-o</code> option to
@@ -2929,7 +2929,7 @@ <h3 class="callout-title">Fixing FastQC to use our own output file names</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" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <p>This is one solution, using <code>-o .</code> to tell FastQC to
 produce the files in the current directory, then explicitly renaming
@@ -3143,7 +3143,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <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">
 <pre class="source"><code>rule salmon_quant:
     output: directory("salmon.{sample}")
@@ -3214,7 +3214,7 @@ <h3 class="callout-title">Adding a MultiQC rule</h3>
 <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">
 <pre class="source"><code>rule multiqc:
     output: directory('multiqc_out')
@@ -3274,7 +3274,7 @@ <h3 class="callout-title">Fixing Kallisto</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">
 <pre class="source"><code># Kallisto quantification of one sample, with log capture.
 rule kallisto_quant:
@@ -3336,7 +3336,7 @@ <h3 class="callout-title">Making the MultiQC rule more robust</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">
 <p>This solution will work with the version of <em>kallisto_quant</em>
 in the solution above.</p>
@@ -3482,7 +3482,7 @@ <h3 class="callout-title">Adding a parameter to the
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <pre class="source"><code>rule salmon_index:
     output:
@@ -3585,7 +3585,7 @@ <h3 class="callout-title">Making the parameter of a rule configurable</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <p>Rule is as before, aside from:</p>
 <pre class="source"><code><span><span class="va">params</span><span class="op">:</span></span>
@@ -3662,7 +3662,7 @@ <h3 class="callout-title">Making the conditions and replicates into configurable
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <p>In <em>config.yaml</em> add the lines:</p>
 <pre class="source"><code>conditions: ["etoh60", "temp33", "ref"]
@@ -4187,7 +4187,7 @@ <h3 class="callout-title">Queryting and installing Conda packages</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>There are several ways of doing this, but one using the commands
@@ -4332,7 +4332,7 @@ <h3 class="callout-title">Using an older version of Salmon</h3>
 <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">
 <p>The first thing that we need is an appropriate YAML file. It’s
 possible to write one from scratch in a text editor, but for this answer
@@ -4528,7 +4528,7 @@ <h3 class="callout-title">Running the Bash script</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">
 <p>The commands to build and activate the Conda env can be found in the
 “Conda Integration” chapter.</p>
@@ -4681,7 +4681,7 @@ <h3 class="callout-title">Challenge - building a full Snakemake workflow</h3>
 <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">
 <p>A sample solution to this exercise <a href="../files/assembly_with_conda.Snakefile">is available here</a>, along
 with a suitable <a href="../files/assembly_conda_env.yaml">Conda
@@ -5406,8 +5406,8 @@ <h3 class="callout-title">Key Points</h3>
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   "dateCreated": "2021-03-26",
-  "dateModified": "2024-08-27",
-  "datePublished": "2024-08-27"
+  "dateModified": "2024-09-03",
+  "datePublished": "2024-09-03"
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   </script><script>
diff --git a/instructor/discuss.html b/instructor/discuss.html
index b858c54..8cce4e6 100644
--- a/instructor/discuss.html
+++ b/instructor/discuss.html
@@ -454,7 +454,7 @@ <h1>Discussion</h1>
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   "dateCreated": "2021-03-26",
   "dateModified": "2024-02-22",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
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   </script><script>
diff --git a/instructor/images.html b/instructor/images.html
index 056ce48..49d6f02 100644
--- a/instructor/images.html
+++ b/instructor/images.html
@@ -539,8 +539,8 @@ <h3 id="11-assembly_challenge-figure-1">Figure 1</h3>
   "url": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/images.html",
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/images.html",
   "dateCreated": "2021-03-26",
-  "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 c4cbf15..fb9f7fd 100644
--- a/instructor/index.html
+++ b/instructor/index.html
@@ -755,8 +755,8 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
   "url": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/index.html",
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   "dateCreated": "2021-03-26",
-  "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 bd81917..dd46719 100644
--- a/instructor/instructor-notes.html
+++ b/instructor/instructor-notes.html
@@ -601,8 +601,8 @@ <h2 id="episode-03---chaining-rules">Episode 03 - Chaining rules<a class="anchor
   "url": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/instructor-notes.html",
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/instructor-notes.html",
   "dateCreated": "2021-03-26",
-  "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 97464c0..015c2d8 100644
--- a/instructor/key-points.html
+++ b/instructor/key-points.html
@@ -634,8 +634,8 @@ <h2 class="accordion-header" id="flush-headingTwelve">
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   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/key-points.html",
   "dateCreated": "2021-03-26",
-  "dateModified": "2024-08-27",
-  "datePublished": "2024-08-27"
+  "dateModified": "2024-09-03",
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/paper.html b/instructor/paper.html
index 1003886..814afa2 100644
--- a/instructor/paper.html
+++ b/instructor/paper.html
@@ -491,7 +491,7 @@ <h1 id="achnowledgements">Achnowledgements<a class="anchor" aria-label="anchor"
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   "dateCreated": "2021-03-26",
   "dateModified": "2024-02-22",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/instructor/profiles.html b/instructor/profiles.html
index a6dd896..6bfbcf1 100644
--- a/instructor/profiles.html
+++ b/instructor/profiles.html
@@ -479,8 +479,8 @@ <h1>Learner Profiles</h1>
   "url": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/profiles.html",
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/profiles.html",
   "dateCreated": "2021-03-26",
-  "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 bd88bc2..c52aed8 100644
--- a/instructor/reference.html
+++ b/instructor/reference.html
@@ -498,7 +498,7 @@ <h1>Glossary</h1>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/reference.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-02-22",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/key-points.html b/key-points.html
index 9447f17..972294b 100644
--- a/key-points.html
+++ b/key-points.html
@@ -632,8 +632,8 @@ <h2 class="accordion-header" id="flush-headingTwelve">
   "url": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/key-points.html",
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/key-points.html",
   "dateCreated": "2021-03-26",
-  "dateModified": "2024-08-27",
-  "datePublished": "2024-08-27"
+  "dateModified": "2024-09-03",
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/paper.html b/paper.html
index c02d908..f9e5b72 100644
--- a/paper.html
+++ b/paper.html
@@ -489,7 +489,7 @@ <h1 id="achnowledgements">Achnowledgements<a class="anchor" aria-label="anchor"
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/paper.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-02-22",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>
diff --git a/pkgdown.yml b/pkgdown.yml
index c3cde97..384d787 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,4 +2,4 @@ pandoc: 2.19.2
 pkgdown: 2.1.0
 pkgdown_sha: ~
 articles: {}
-last_built: 2024-08-27T00:55Z
+last_built: 2024-09-03T00:56Z
diff --git a/profiles.html b/profiles.html
index 156d611..0ceec30 100644
--- a/profiles.html
+++ b/profiles.html
@@ -479,8 +479,8 @@ <h1>Learner Profiles</h1>
   "url": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/profiles.html",
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/profiles.html",
   "dateCreated": "2021-03-26",
-  "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 73a2d38..25158dc 100644
--- a/reference.html
+++ b/reference.html
@@ -496,7 +496,7 @@ <h1>Glossary</h1>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/reference.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-02-22",
-  "datePublished": "2024-08-27"
+  "datePublished": "2024-09-03"
 }
 
   </script><script>