From 738b639aaa5bd7416b84614a1b95a038836ad273 Mon Sep 17 00:00:00 2001
From: GitHub Actions <actions@github.com>
Date: Tue, 13 Aug 2024 00:56:14 +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                |  8 ++---
 04-the_dag.html                       |  6 ++--
 05-expansion.html                     |  2 +-
 06-awkward_programs.html              |  8 ++---
 07-finished-workflow.html             | 10 +++---
 08-configuring.html                   |  8 ++---
 09-performance.html                   |  6 ++--
 10-conda_integration.html             |  6 ++--
 11-assembly_challenge.html            |  6 ++--
 12-cleaning_up.html                   |  2 +-
 13-quoting.html                       |  6 ++--
 404.html                              |  4 +--
 CODE_OF_CONDUCT.html                  |  2 +-
 LICENSE.html                          |  2 +-
 aio.html                              | 50 +++++++++++++--------------
 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     |  8 ++---
 instructor/04-the_dag.html            |  6 ++--
 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        |  6 ++--
 instructor/10-conda_integration.html  |  6 ++--
 instructor/11-assembly_challenge.html |  6 ++--
 instructor/12-cleaning_up.html        |  2 +-
 instructor/13-quoting.html            |  6 ++--
 instructor/404.html                   |  4 +--
 instructor/CODE_OF_CONDUCT.html       |  2 +-
 instructor/LICENSE.html               |  2 +-
 instructor/aio.html                   | 50 +++++++++++++--------------
 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, 157 insertions(+), 157 deletions(-)

diff --git a/01-introduction.html b/01-introduction.html
index 2dcd539..d30637d 100644
--- a/01-introduction.html
+++ b/01-introduction.html
@@ -756,7 +756,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/01-introduction.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-02-22",
-  "datePublished": "2024-08-06"
+  "datePublished": "2024-08-13"
 }
 
   </script><script>
diff --git a/02-placeholders.html b/02-placeholders.html
index 1f32c50..6fa1cb6 100644
--- a/02-placeholders.html
+++ b/02-placeholders.html
@@ -816,7 +816,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/02-placeholders.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-02-23",
-  "datePublished": "2024-08-06"
+  "datePublished": "2024-08-13"
 }
 
   </script><script>
diff --git a/03-chaining_rules.html b/03-chaining_rules.html
index 6368738..f322a7c 100644
--- a/03-chaining_rules.html
+++ b/03-chaining_rules.html
@@ -545,7 +545,7 @@ <h3 class="callout-title">Thinking about your own workflows<a class="anchor" ari
 <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"> A sample answer based on brewing a mug of tea. </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><em>TODO - draw this out too.</em></p>
 <pre><code>"Boil Water" : input=cold water, output=hot water
@@ -658,7 +658,7 @@ <h3 class="callout-title">Running the kallisto_quant rule<a class="anchor" aria-
 <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="cb7">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -705,7 +705,7 @@ <h3 class="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="#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>The rule you write could look something like this, but there are many
 variations that will work just as well. Since there is only one
@@ -943,7 +943,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/03-chaining_rules.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-03-01",
-  "datePublished": "2024-08-06"
+  "datePublished": "2024-08-13"
 }
 
   </script><script>
diff --git a/04-the_dag.html b/04-the_dag.html
index 013a050..7deddc1 100644
--- a/04-the_dag.html
+++ b/04-the_dag.html
@@ -493,7 +493,7 @@ <h3 class="callout-title">How many jobs?<a class="anchor" aria-label="anchor" hr
 <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>10 in total: 3 * kallisto_quant // 6 * trimreads // 1 *
 kallisto_index // 0 * countreads</p>
@@ -700,7 +700,7 @@ <h3 class="callout-title">Visualising the effect of the <code>-R</code>
 <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>This is a way to make the Kallisto result in the first place:</p>
 <div class="codewrapper sourceCode" id="cb13">
@@ -841,7 +841,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/04-the_dag.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-03-11",
-  "datePublished": "2024-08-06"
+  "datePublished": "2024-08-13"
 }
 
   </script><script>
diff --git a/05-expansion.html b/05-expansion.html
index d2634b1..d6d9c06 100644
--- a/05-expansion.html
+++ b/05-expansion.html
@@ -972,7 +972,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/05-expansion.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-02-23",
-  "datePublished": "2024-08-06"
+  "datePublished": "2024-08-13"
 }
 
   </script><script>
diff --git a/06-awkward_programs.html b/06-awkward_programs.html
index 54fb287..07ebf8a 100644
--- a/06-awkward_programs.html
+++ b/06-awkward_programs.html
@@ -533,7 +533,7 @@ <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
@@ -590,7 +590,7 @@ <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
@@ -725,7 +725,7 @@ <h3 class="callout-title">Fixing FastQC to use our own output file names<a class
 <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
@@ -870,7 +870,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/06-awkward_programs.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-03-01",
-  "datePublished": "2024-08-06"
+  "datePublished": "2024-08-13"
 }
 
   </script><script>
diff --git a/07-finished-workflow.html b/07-finished-workflow.html
index 97d1a6c..47cc5ea 100644
--- a/07-finished-workflow.html
+++ b/07-finished-workflow.html
@@ -512,7 +512,7 @@ <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" 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_quant:
     output: directory("salmon.{sample}")
@@ -581,7 +581,7 @@ <h3 class="callout-title">Adding a MultiQC rule<a class="anchor" aria-label="anc
 <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">
 <pre class="source"><code>rule multiqc:
     output: directory('multiqc_out')
@@ -640,7 +640,7 @@ <h3 class="callout-title">Fixing Kallisto<a class="anchor" aria-label="anchor" h
 <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">
 <pre class="source"><code># Kallisto quantification of one sample, with log capture.
 rule kallisto_quant:
@@ -701,7 +701,7 @@ <h3 class="callout-title">Making the MultiQC rule more robust<a class="anchor" a
 <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" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <p>This solution will work with the version of <em>kallisto_quant</em>
 in the solution above.</p>
@@ -818,7 +818,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/07-finished-workflow.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-03-01",
-  "datePublished": "2024-08-06"
+  "datePublished": "2024-08-13"
 }
 
   </script><script>
diff --git a/08-configuring.html b/08-configuring.html
index 4227e76..0295aa8 100644
--- a/08-configuring.html
+++ b/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:
@@ -578,7 +578,7 @@ <h3 class="callout-title">Making the parameter of a rule configurable<a class="a
 <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>
@@ -652,7 +652,7 @@ <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"]
@@ -763,7 +763,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/08-configuring.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-03-11",
-  "datePublished": "2024-08-06"
+  "datePublished": "2024-08-13"
 }
 
   </script><script>
diff --git a/09-performance.html b/09-performance.html
index bfafa2a..82eeee7 100644
--- a/09-performance.html
+++ b/09-performance.html
@@ -520,7 +520,7 @@ <h3 class="callout-title">Measuring how concurrency affects execution time<a cla
 <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>The time will vary depending on the system configuration but
 somewhere around 30 seconds is expected, and this should reduce to
@@ -600,7 +600,7 @@ <h3 class="callout-title">Getting other programs to run with multiple threads<a
 <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>For <em>salmon_quant</em>, <code>-p {threads}</code> or equivalently
 <code>--threads {threads}</code> will work.</p>
@@ -740,7 +740,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/09-performance.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-03-01",
-  "datePublished": "2024-08-06"
+  "datePublished": "2024-08-13"
 }
 
   </script><script>
diff --git a/10-conda_integration.html b/10-conda_integration.html
index 8525c3d..02cd1a6 100644
--- a/10-conda_integration.html
+++ b/10-conda_integration.html
@@ -538,7 +538,7 @@ <h3 class="callout-title">Queryting and installing Conda packages<a class="ancho
 <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>
@@ -679,7 +679,7 @@ <h3 class="callout-title">Using an older version of Salmon<a class="anchor" aria
 <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
@@ -834,7 +834,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/10-conda_integration.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-03-11",
-  "datePublished": "2024-08-06"
+  "datePublished": "2024-08-13"
 }
 
   </script><script>
diff --git a/11-assembly_challenge.html b/11-assembly_challenge.html
index ea62ca3..ff505f3 100644
--- a/11-assembly_challenge.html
+++ b/11-assembly_challenge.html
@@ -489,7 +489,7 @@ <h3 class="callout-title">Running the Bash script<a class="anchor" aria-label="a
 <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>The commands to build and activate the Conda env can be found in the
 “Conda Integration” chapter.</p>
@@ -620,7 +620,7 @@ <h3 class="callout-title">Challenge - building a full Snakemake workflow<a class
 <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>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
@@ -709,7 +709,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/11-assembly_challenge.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-03-01",
-  "datePublished": "2024-08-06"
+  "datePublished": "2024-08-13"
 }
 
   </script><script>
diff --git a/12-cleaning_up.html b/12-cleaning_up.html
index a2edd3a..54fd780 100644
--- a/12-cleaning_up.html
+++ b/12-cleaning_up.html
@@ -793,7 +793,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/12-cleaning_up.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-03-11",
-  "datePublished": "2024-08-06"
+  "datePublished": "2024-08-13"
 }
 
   </script><script>
diff --git a/13-quoting.html b/13-quoting.html
index edad475..aaaae95 100644
--- a/13-quoting.html
+++ b/13-quoting.html
@@ -543,7 +543,7 @@ <h3 class="callout-title">Adding a ᠎ ᠎ <em>lenreads</em> ᠎ ᠎ rule<a cl
 <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>It won’t work. Snakemake assumes that all parts of the string in
 {curlies} are placeholders. The error will say something like
@@ -628,7 +628,7 @@ <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="#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 just involves adding <code>:q</code> to a whole bunch of
 placeholders. Unless you are very diligent it will probably take a few
@@ -740,7 +740,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/13-quoting.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-03-01",
-  "datePublished": "2024-08-06"
+  "datePublished": "2024-08-13"
 }
 
   </script><script>
diff --git a/404.html b/404.html
index 54428d3..36ea269 100644
--- a/404.html
+++ b/404.html
@@ -452,8 +452,8 @@ <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": "2024-08-06",
-  "datePublished": "2024-08-06"
+  "dateModified": "2024-08-13",
+  "datePublished": "2024-08-13"
 }
 
   </script><script>
diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html
index 680e26b..b6efc77 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": "2024-08-06"
+  "datePublished": "2024-08-13"
 }
 
   </script><script>
diff --git a/LICENSE.html b/LICENSE.html
index 6f35460..edc9e2f 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -565,7 +565,7 @@ <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": "2024-08-06"
+  "datePublished": "2024-08-13"
 }
 
   </script><script>
diff --git a/aio.html b/aio.html
index 3f87489..9d76f56 100644
--- a/aio.html
+++ b/aio.html
@@ -1332,7 +1332,7 @@ <h3 class="callout-title">Thinking about your own workflows<a class="anchor" ari
 <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"> A sample answer based on brewing a mug of tea. </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><em>TODO - draw this out too.</em></p>
 <pre><code>"Boil Water" : input=cold water, output=hot water
@@ -1453,7 +1453,7 @@ <h3 class="callout-title">Running the kallisto_quant rule<a class="anchor" aria-
 <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="cb7">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1500,7 +1500,7 @@ <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="#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>The rule you write could look something like this, but there are many
 variations that will work just as well. Since there is only one
@@ -1790,7 +1790,7 @@ <h3 class="callout-title">How many jobs?<a class="anchor" aria-label="anchor" hr
 <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>10 in total: 3 * kallisto_quant // 6 * trimreads // 1 *
 kallisto_index // 0 * countreads</p>
@@ -2009,7 +2009,7 @@ <h3 class="callout-title">Visualising the effect of the <code>-R</code>
 <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>This is a way to make the Kallisto result in the first place:</p>
 <div class="codewrapper sourceCode" id="cb13">
@@ -2783,7 +2783,7 @@ <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
@@ -2841,7 +2841,7 @@ <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
@@ -2978,7 +2978,7 @@ <h3 class="callout-title">Fixing FastQC to use our own output file names<a class
 <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
@@ -3197,7 +3197,7 @@ <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" 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_quant:
     output: directory("salmon.{sample}")
@@ -3270,7 +3270,7 @@ <h3 class="callout-title">Adding a MultiQC rule<a class="anchor" aria-label="anc
 <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">
 <pre class="source"><code>rule multiqc:
     output: directory('multiqc_out')
@@ -3331,7 +3331,7 @@ <h3 class="callout-title">Fixing Kallisto<a class="anchor" aria-label="anchor" h
 <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">
 <pre class="source"><code># Kallisto quantification of one sample, with log capture.
 rule kallisto_quant:
@@ -3394,7 +3394,7 @@ <h3 class="callout-title">Making the MultiQC rule more robust<a class="anchor" a
 <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" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <p>This solution will work with the version of <em>kallisto_quant</em>
 in the solution above.</p>
@@ -3542,7 +3542,7 @@ <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:
@@ -3648,7 +3648,7 @@ <h3 class="callout-title">Making the parameter of a rule configurable<a class="a
 <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>
@@ -3726,7 +3726,7 @@ <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"]
@@ -3919,7 +3919,7 @@ <h3 class="callout-title">Measuring how concurrency affects execution time<a cla
 <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>The time will vary depending on the system configuration but
 somewhere around 30 seconds is expected, and this should reduce to
@@ -4006,7 +4006,7 @@ <h3 class="callout-title">Getting other programs to run with multiple threads<a
 <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>For <em>salmon_quant</em>, <code>-p {threads}</code> or equivalently
 <code>--threads {threads}</code> will work.</p>
@@ -4263,7 +4263,7 @@ <h3 class="callout-title">Queryting and installing Conda packages<a class="ancho
 <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
@@ -4410,7 +4410,7 @@ <h3 class="callout-title">Using an older version of Salmon<a class="anchor" aria
 <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
@@ -4609,7 +4609,7 @@ <h3 class="callout-title">Running the Bash script<a class="anchor" aria-label="a
 <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>The commands to build and activate the Conda env can be found in the
 “Conda Integration” chapter.</p>
@@ -4764,7 +4764,7 @@ <h3 class="callout-title">Challenge - building a full Snakemake workflow<a class
 <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>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
@@ -5313,7 +5313,7 @@ <h3 class="callout-title">Adding a ᠎ ᠎ <em>lenreads</em> ᠎ ᠎ rule<a cl
 <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>It won’t work. Snakemake assumes that all parts of the string in
 {curlies} are placeholders. The error will say something like
@@ -5400,7 +5400,7 @@ <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="#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 just involves adding <code>:q</code> to a whole bunch of
 placeholders. Unless you are very diligent it will probably take a few
@@ -5503,8 +5503,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "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": "2024-08-06",
-  "datePublished": "2024-08-06"
+  "dateModified": "2024-08-13",
+  "datePublished": "2024-08-13"
 }
 
   </script><script>
diff --git a/discuss.html b/discuss.html
index 160ac2b..11d46d7 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": "2024-08-06"
+  "datePublished": "2024-08-13"
 }
 
   </script><script>
diff --git a/images.html b/images.html
index 6d66ba8..1b1a916 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": "2024-08-06",
-  "datePublished": "2024-08-06"
+  "dateModified": "2024-08-13",
+  "datePublished": "2024-08-13"
 }
 
   </script><script>
diff --git a/index.html b/index.html
index 38a6cea..6a34cfe 100644
--- a/index.html
+++ b/index.html
@@ -626,8 +626,8 @@ <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": "2024-08-06",
-  "datePublished": "2024-08-06"
+  "dateModified": "2024-08-13",
+  "datePublished": "2024-08-13"
 }
 
   </script><script>
diff --git a/instructor-notes.html b/instructor-notes.html
index 6335f72..c0c083c 100644
--- a/instructor-notes.html
+++ b/instructor-notes.html
@@ -587,8 +587,8 @@ <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": "2024-08-06",
-  "datePublished": "2024-08-06"
+  "dateModified": "2024-08-13",
+  "datePublished": "2024-08-13"
 }
 
   </script><script>
diff --git a/instructor/01-introduction.html b/instructor/01-introduction.html
index d35b6dd..b390439 100644
--- a/instructor/01-introduction.html
+++ b/instructor/01-introduction.html
@@ -758,7 +758,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/01-introduction.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-02-22",
-  "datePublished": "2024-08-06"
+  "datePublished": "2024-08-13"
 }
 
   </script><script>
diff --git a/instructor/02-placeholders.html b/instructor/02-placeholders.html
index b3a5cdf..012858d 100644
--- a/instructor/02-placeholders.html
+++ b/instructor/02-placeholders.html
@@ -818,7 +818,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/02-placeholders.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-02-23",
-  "datePublished": "2024-08-06"
+  "datePublished": "2024-08-13"
 }
 
   </script><script>
diff --git a/instructor/03-chaining_rules.html b/instructor/03-chaining_rules.html
index f7c9179..2d5e26d 100644
--- a/instructor/03-chaining_rules.html
+++ b/instructor/03-chaining_rules.html
@@ -547,7 +547,7 @@ <h3 class="callout-title">Thinking about your own workflows<a class="anchor" ari
 <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"> A sample answer based on brewing a mug of tea. </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><em>TODO - draw this out too.</em></p>
 <pre><code>"Boil Water" : input=cold water, output=hot water
@@ -660,7 +660,7 @@ <h3 class="callout-title">Running the kallisto_quant rule<a class="anchor" aria-
 <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="cb7">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -707,7 +707,7 @@ <h3 class="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="#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>The rule you write could look something like this, but there are many
 variations that will work just as well. Since there is only one
@@ -945,7 +945,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/03-chaining_rules.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-03-01",
-  "datePublished": "2024-08-06"
+  "datePublished": "2024-08-13"
 }
 
   </script><script>
diff --git a/instructor/04-the_dag.html b/instructor/04-the_dag.html
index 2b200cf..2efabf0 100644
--- a/instructor/04-the_dag.html
+++ b/instructor/04-the_dag.html
@@ -495,7 +495,7 @@ <h3 class="callout-title">How many jobs?<a class="anchor" aria-label="anchor" hr
 <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>10 in total: 3 * kallisto_quant // 6 * trimreads // 1 *
 kallisto_index // 0 * countreads</p>
@@ -702,7 +702,7 @@ <h3 class="callout-title">Visualising the effect of the <code>-R</code>
 <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>This is a way to make the Kallisto result in the first place:</p>
 <div class="codewrapper sourceCode" id="cb13">
@@ -843,7 +843,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/04-the_dag.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-03-11",
-  "datePublished": "2024-08-06"
+  "datePublished": "2024-08-13"
 }
 
   </script><script>
diff --git a/instructor/05-expansion.html b/instructor/05-expansion.html
index 3b600b0..e08ccdd 100644
--- a/instructor/05-expansion.html
+++ b/instructor/05-expansion.html
@@ -974,7 +974,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/05-expansion.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-02-23",
-  "datePublished": "2024-08-06"
+  "datePublished": "2024-08-13"
 }
 
   </script><script>
diff --git a/instructor/06-awkward_programs.html b/instructor/06-awkward_programs.html
index b6d56aa..3050949 100644
--- a/instructor/06-awkward_programs.html
+++ b/instructor/06-awkward_programs.html
@@ -535,7 +535,7 @@ <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
@@ -592,7 +592,7 @@ <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
@@ -727,7 +727,7 @@ <h3 class="callout-title">Fixing FastQC to use our own output file names<a class
 <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
@@ -872,7 +872,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/06-awkward_programs.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-03-01",
-  "datePublished": "2024-08-06"
+  "datePublished": "2024-08-13"
 }
 
   </script><script>
diff --git a/instructor/07-finished-workflow.html b/instructor/07-finished-workflow.html
index 5a842e8..71c6787 100644
--- a/instructor/07-finished-workflow.html
+++ b/instructor/07-finished-workflow.html
@@ -514,7 +514,7 @@ <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" 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_quant:
     output: directory("salmon.{sample}")
@@ -583,7 +583,7 @@ <h3 class="callout-title">Adding a MultiQC rule<a class="anchor" aria-label="anc
 <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">
 <pre class="source"><code>rule multiqc:
     output: directory('multiqc_out')
@@ -642,7 +642,7 @@ <h3 class="callout-title">Fixing Kallisto<a class="anchor" aria-label="anchor" h
 <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">
 <pre class="source"><code># Kallisto quantification of one sample, with log capture.
 rule kallisto_quant:
@@ -703,7 +703,7 @@ <h3 class="callout-title">Making the MultiQC rule more robust<a class="anchor" a
 <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" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <p>This solution will work with the version of <em>kallisto_quant</em>
 in the solution above.</p>
@@ -820,7 +820,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/07-finished-workflow.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-03-01",
-  "datePublished": "2024-08-06"
+  "datePublished": "2024-08-13"
 }
 
   </script><script>
diff --git a/instructor/08-configuring.html b/instructor/08-configuring.html
index 892d676..978df49 100644
--- a/instructor/08-configuring.html
+++ b/instructor/08-configuring.html
@@ -478,7 +478,7 @@ <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:
@@ -580,7 +580,7 @@ <h3 class="callout-title">Making the parameter of a rule configurable<a class="a
 <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>
@@ -654,7 +654,7 @@ <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"]
@@ -765,7 +765,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/08-configuring.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-03-11",
-  "datePublished": "2024-08-06"
+  "datePublished": "2024-08-13"
 }
 
   </script><script>
diff --git a/instructor/09-performance.html b/instructor/09-performance.html
index fc69115..9c94613 100644
--- a/instructor/09-performance.html
+++ b/instructor/09-performance.html
@@ -522,7 +522,7 @@ <h3 class="callout-title">Measuring how concurrency affects execution time<a cla
 <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>The time will vary depending on the system configuration but
 somewhere around 30 seconds is expected, and this should reduce to
@@ -602,7 +602,7 @@ <h3 class="callout-title">Getting other programs to run with multiple threads<a
 <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>For <em>salmon_quant</em>, <code>-p {threads}</code> or equivalently
 <code>--threads {threads}</code> will work.</p>
@@ -742,7 +742,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/09-performance.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-03-01",
-  "datePublished": "2024-08-06"
+  "datePublished": "2024-08-13"
 }
 
   </script><script>
diff --git a/instructor/10-conda_integration.html b/instructor/10-conda_integration.html
index 05bdb6e..c5dae5d 100644
--- a/instructor/10-conda_integration.html
+++ b/instructor/10-conda_integration.html
@@ -540,7 +540,7 @@ <h3 class="callout-title">Queryting and installing Conda packages<a class="ancho
 <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>
@@ -681,7 +681,7 @@ <h3 class="callout-title">Using an older version of Salmon<a class="anchor" aria
 <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
@@ -836,7 +836,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/10-conda_integration.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-03-11",
-  "datePublished": "2024-08-06"
+  "datePublished": "2024-08-13"
 }
 
   </script><script>
diff --git a/instructor/11-assembly_challenge.html b/instructor/11-assembly_challenge.html
index 567a556..d8b0668 100644
--- a/instructor/11-assembly_challenge.html
+++ b/instructor/11-assembly_challenge.html
@@ -491,7 +491,7 @@ <h3 class="callout-title">Running the Bash script<a class="anchor" aria-label="a
 <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>The commands to build and activate the Conda env can be found in the
 “Conda Integration” chapter.</p>
@@ -622,7 +622,7 @@ <h3 class="callout-title">Challenge - building a full Snakemake workflow<a class
 <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>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
@@ -711,7 +711,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/11-assembly_challenge.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-03-01",
-  "datePublished": "2024-08-06"
+  "datePublished": "2024-08-13"
 }
 
   </script><script>
diff --git a/instructor/12-cleaning_up.html b/instructor/12-cleaning_up.html
index 430341f..07540f6 100644
--- a/instructor/12-cleaning_up.html
+++ b/instructor/12-cleaning_up.html
@@ -795,7 +795,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/12-cleaning_up.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-03-11",
-  "datePublished": "2024-08-06"
+  "datePublished": "2024-08-13"
 }
 
   </script><script>
diff --git a/instructor/13-quoting.html b/instructor/13-quoting.html
index 6e2764d..fa717e9 100644
--- a/instructor/13-quoting.html
+++ b/instructor/13-quoting.html
@@ -545,7 +545,7 @@ <h3 class="callout-title">Adding a ᠎ ᠎ <em>lenreads</em> ᠎ ᠎ rule<a cl
 <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>It won’t work. Snakemake assumes that all parts of the string in
 {curlies} are placeholders. The error will say something like
@@ -630,7 +630,7 @@ <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="#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 just involves adding <code>:q</code> to a whole bunch of
 placeholders. Unless you are very diligent it will probably take a few
@@ -742,7 +742,7 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/13-quoting.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-03-01",
-  "datePublished": "2024-08-06"
+  "datePublished": "2024-08-13"
 }
 
   </script><script>
diff --git a/instructor/404.html b/instructor/404.html
index fca1243..395b658 100644
--- a/instructor/404.html
+++ b/instructor/404.html
@@ -452,8 +452,8 @@ <h1>Page not found</h1>
   "url": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/404.html",
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/404.html",
   "dateCreated": "2021-03-26",
-  "dateModified": "2024-08-06",
-  "datePublished": "2024-08-06"
+  "dateModified": "2024-08-13",
+  "datePublished": "2024-08-13"
 }
 
   </script><script>
diff --git a/instructor/CODE_OF_CONDUCT.html b/instructor/CODE_OF_CONDUCT.html
index 681dad1..5afad1b 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": "2024-08-06"
+  "datePublished": "2024-08-13"
 }
 
   </script><script>
diff --git a/instructor/LICENSE.html b/instructor/LICENSE.html
index c872def..89196fb 100644
--- a/instructor/LICENSE.html
+++ b/instructor/LICENSE.html
@@ -567,7 +567,7 @@ <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": "2024-08-06"
+  "datePublished": "2024-08-13"
 }
 
   </script><script>
diff --git a/instructor/aio.html b/instructor/aio.html
index 7f89058..1d1d231 100644
--- a/instructor/aio.html
+++ b/instructor/aio.html
@@ -1337,7 +1337,7 @@ <h3 class="callout-title">Thinking about your own workflows<a class="anchor" ari
 <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"> A sample answer based on brewing a mug of tea. </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><em>TODO - draw this out too.</em></p>
 <pre><code>"Boil Water" : input=cold water, output=hot water
@@ -1458,7 +1458,7 @@ <h3 class="callout-title">Running the kallisto_quant rule<a class="anchor" aria-
 <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="cb7">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1505,7 +1505,7 @@ <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="#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>The rule you write could look something like this, but there are many
 variations that will work just as well. Since there is only one
@@ -1796,7 +1796,7 @@ <h3 class="callout-title">How many jobs?<a class="anchor" aria-label="anchor" hr
 <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>10 in total: 3 * kallisto_quant // 6 * trimreads // 1 *
 kallisto_index // 0 * countreads</p>
@@ -2015,7 +2015,7 @@ <h3 class="callout-title">Visualising the effect of the <code>-R</code>
 <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>This is a way to make the Kallisto result in the first place:</p>
 <div class="codewrapper sourceCode" id="cb13">
@@ -2791,7 +2791,7 @@ <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
@@ -2849,7 +2849,7 @@ <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
@@ -2986,7 +2986,7 @@ <h3 class="callout-title">Fixing FastQC to use our own output file names<a class
 <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
@@ -3206,7 +3206,7 @@ <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" 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_quant:
     output: directory("salmon.{sample}")
@@ -3279,7 +3279,7 @@ <h3 class="callout-title">Adding a MultiQC rule<a class="anchor" aria-label="anc
 <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">
 <pre class="source"><code>rule multiqc:
     output: directory('multiqc_out')
@@ -3340,7 +3340,7 @@ <h3 class="callout-title">Fixing Kallisto<a class="anchor" aria-label="anchor" h
 <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">
 <pre class="source"><code># Kallisto quantification of one sample, with log capture.
 rule kallisto_quant:
@@ -3403,7 +3403,7 @@ <h3 class="callout-title">Making the MultiQC rule more robust<a class="anchor" a
 <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" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <p>This solution will work with the version of <em>kallisto_quant</em>
 in the solution above.</p>
@@ -3552,7 +3552,7 @@ <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:
@@ -3658,7 +3658,7 @@ <h3 class="callout-title">Making the parameter of a rule configurable<a class="a
 <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>
@@ -3736,7 +3736,7 @@ <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"]
@@ -3930,7 +3930,7 @@ <h3 class="callout-title">Measuring how concurrency affects execution time<a cla
 <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>The time will vary depending on the system configuration but
 somewhere around 30 seconds is expected, and this should reduce to
@@ -4017,7 +4017,7 @@ <h3 class="callout-title">Getting other programs to run with multiple threads<a
 <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>For <em>salmon_quant</em>, <code>-p {threads}</code> or equivalently
 <code>--threads {threads}</code> will work.</p>
@@ -4275,7 +4275,7 @@ <h3 class="callout-title">Queryting and installing Conda packages<a class="ancho
 <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
@@ -4422,7 +4422,7 @@ <h3 class="callout-title">Using an older version of Salmon<a class="anchor" aria
 <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
@@ -4622,7 +4622,7 @@ <h3 class="callout-title">Running the Bash script<a class="anchor" aria-label="a
 <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>The commands to build and activate the Conda env can be found in the
 “Conda Integration” chapter.</p>
@@ -4777,7 +4777,7 @@ <h3 class="callout-title">Challenge - building a full Snakemake workflow<a class
 <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>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
@@ -5328,7 +5328,7 @@ <h3 class="callout-title">Adding a ᠎ ᠎ <em>lenreads</em> ᠎ ᠎ rule<a cl
 <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>It won’t work. Snakemake assumes that all parts of the string in
 {curlies} are placeholders. The error will say something like
@@ -5415,7 +5415,7 @@ <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="#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 just involves adding <code>:q</code> to a whole bunch of
 placeholders. Unless you are very diligent it will probably take a few
@@ -5518,8 +5518,8 @@ <h3 class="callout-title">Key Points<a class="anchor" aria-label="anchor" href="
   "url": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/aio.html",
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/aio.html",
   "dateCreated": "2021-03-26",
-  "dateModified": "2024-08-06",
-  "datePublished": "2024-08-06"
+  "dateModified": "2024-08-13",
+  "datePublished": "2024-08-13"
 }
 
   </script><script>
diff --git a/instructor/discuss.html b/instructor/discuss.html
index 5c5a18c..cc3ed6c 100644
--- a/instructor/discuss.html
+++ b/instructor/discuss.html
@@ -454,7 +454,7 @@ <h1>Discussion</h1>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/discuss.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-02-22",
-  "datePublished": "2024-08-06"
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 }
 
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diff --git a/instructor/images.html b/instructor/images.html
index 87ba281..50fe1f3 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": "2024-08-06",
-  "datePublished": "2024-08-06"
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 }
 
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diff --git a/instructor/index.html b/instructor/index.html
index df5b189..0c335d0 100644
--- a/instructor/index.html
+++ b/instructor/index.html
@@ -761,8 +761,8 @@ <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",
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/index.html",
   "dateCreated": "2021-03-26",
-  "dateModified": "2024-08-06",
-  "datePublished": "2024-08-06"
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 }
 
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diff --git a/instructor/instructor-notes.html b/instructor/instructor-notes.html
index 9a51542..1956d7a 100644
--- a/instructor/instructor-notes.html
+++ b/instructor/instructor-notes.html
@@ -602,8 +602,8 @@ <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": "2024-08-06",
-  "datePublished": "2024-08-06"
+  "dateModified": "2024-08-13",
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 }
 
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diff --git a/instructor/key-points.html b/instructor/key-points.html
index 0f4fa8f..fdc51b9 100644
--- a/instructor/key-points.html
+++ b/instructor/key-points.html
@@ -634,8 +634,8 @@ <h2 class="accordion-header" id="flush-headingTwelve">
   "url": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/key-points.html",
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/key-points.html",
   "dateCreated": "2021-03-26",
-  "dateModified": "2024-08-06",
-  "datePublished": "2024-08-06"
+  "dateModified": "2024-08-13",
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 }
 
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diff --git a/instructor/paper.html b/instructor/paper.html
index 7b5bedb..ae1d149 100644
--- a/instructor/paper.html
+++ b/instructor/paper.html
@@ -491,7 +491,7 @@ <h1 id="achnowledgements">Achnowledgements<a class="anchor" aria-label="anchor"
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/paper.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-02-22",
-  "datePublished": "2024-08-06"
+  "datePublished": "2024-08-13"
 }
 
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diff --git a/instructor/profiles.html b/instructor/profiles.html
index ca8d208..31525d2 100644
--- a/instructor/profiles.html
+++ b/instructor/profiles.html
@@ -482,8 +482,8 @@ <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": "2024-08-06",
-  "datePublished": "2024-08-06"
+  "dateModified": "2024-08-13",
+  "datePublished": "2024-08-13"
 }
 
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diff --git a/instructor/reference.html b/instructor/reference.html
index 97c2a17..b462baa 100644
--- a/instructor/reference.html
+++ b/instructor/reference.html
@@ -499,7 +499,7 @@ <h1>Glossary</h1>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/reference.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-02-22",
-  "datePublished": "2024-08-06"
+  "datePublished": "2024-08-13"
 }
 
   </script><script>
diff --git a/key-points.html b/key-points.html
index 5548943..3ec032e 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": "2024-08-06",
-  "datePublished": "2024-08-06"
+  "dateModified": "2024-08-13",
+  "datePublished": "2024-08-13"
 }
 
   </script><script>
diff --git a/paper.html b/paper.html
index 131fb47..fb0efdc 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": "2024-08-06"
+  "datePublished": "2024-08-13"
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diff --git a/pkgdown.yml b/pkgdown.yml
index 9be356c..1848336 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,4 +2,4 @@ pandoc: 2.19.2
 pkgdown: 2.1.0
 pkgdown_sha: ~
 articles: {}
-last_built: 2024-08-06T00:54Z
+last_built: 2024-08-13T00:55Z
diff --git a/profiles.html b/profiles.html
index 19a50a3..b642974 100644
--- a/profiles.html
+++ b/profiles.html
@@ -482,8 +482,8 @@ <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": "2024-08-06",
-  "datePublished": "2024-08-06"
+  "dateModified": "2024-08-13",
+  "datePublished": "2024-08-13"
 }
 
   </script><script>
diff --git a/reference.html b/reference.html
index 9c6bd64..512d438 100644
--- a/reference.html
+++ b/reference.html
@@ -497,7 +497,7 @@ <h1>Glossary</h1>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/reference.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-02-22",
-  "datePublished": "2024-08-06"
+  "datePublished": "2024-08-13"
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