From 31a2d01365b23d27deeec2b9df8a54917f2482b7 Mon Sep 17 00:00:00 2001
From: GitHub Actions <actions@github.com>
Date: Tue, 24 Dec 2024 01:01:18 +0000
Subject: [PATCH] site deploy

Auto-generated via `{sandpaper}`
Source  : 1d9c7c37d6de32dbc6321f8fddfff40054213d8c
Branch  : md-outputs
Author  : GitHub Actions <actions@github.com>
Time    : 2024-10-11 17:05:06 +0000
Message : markdown source builds

Auto-generated via `{sandpaper}`
Source  : b5840e5bb15f2da3677521af8445a0f2bce018d4
Branch  : main
Author  : Tim Booth <tim.booth@ed.ac.uk>
Time    : 2024-10-11 17:03:46 +0000
Message : Reformat title
---
 01-introduction.html                  |  2 +-
 02-placeholders.html                  |  8 +++----
 03-chaining_rules.html                |  6 +++---
 04-logs_and_errors.html               |  2 +-
 05-the_dag.html                       |  6 +++---
 06-expansion.html                     |  2 +-
 07-awkward_programs.html              |  2 +-
 08-finished-workflow.html             |  2 +-
 09-configuring.html                   |  8 +++----
 10-performance.html                   |  2 +-
 11-conda_integration.html             |  2 +-
 12-assembly_challenge.html            |  2 +-
 13-cleaning_up.html                   |  6 +++---
 404.html                              |  4 ++--
 B1-quoting.html                       |  2 +-
 CODE_OF_CONDUCT.html                  |  2 +-
 LICENSE.html                          |  2 +-
 aio.html                              | 28 ++++++++++++-------------
 discuss.html                          |  2 +-
 images.html                           |  4 ++--
 index.html                            |  4 ++--
 instructor-notes.html                 |  4 ++--
 instructor/01-introduction.html       |  2 +-
 instructor/02-placeholders.html       |  8 +++----
 instructor/03-chaining_rules.html     |  8 +++----
 instructor/04-logs_and_errors.html    |  2 +-
 instructor/05-the_dag.html            |  6 +++---
 instructor/06-expansion.html          |  2 +-
 instructor/07-awkward_programs.html   |  2 +-
 instructor/08-finished-workflow.html  |  2 +-
 instructor/09-configuring.html        |  8 +++----
 instructor/10-performance.html        |  2 +-
 instructor/11-conda_integration.html  |  2 +-
 instructor/12-assembly_challenge.html |  2 +-
 instructor/13-cleaning_up.html        |  6 +++---
 instructor/404.html                   |  4 ++--
 instructor/B1-quoting.html            |  2 +-
 instructor/CODE_OF_CONDUCT.html       |  2 +-
 instructor/LICENSE.html               |  2 +-
 instructor/aio.html                   | 30 +++++++++++++--------------
 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/prereqs.html               |  2 +-
 instructor/profiles.html              |  4 ++--
 instructor/reference.html             |  2 +-
 key-points.html                       |  4 ++--
 paper.html                            |  2 +-
 pkgdown.yml                           |  2 +-
 prereqs.html                          |  2 +-
 profiles.html                         |  4 ++--
 reference.html                        |  2 +-
 55 files changed, 119 insertions(+), 119 deletions(-)

diff --git a/01-introduction.html b/01-introduction.html
index 5f490f8..7051bbe 100644
--- a/01-introduction.html
+++ b/01-introduction.html
@@ -755,7 +755,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/01-introduction.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-10-07",
-  "datePublished": "2024-12-17"
+  "datePublished": "2024-12-24"
 }
 
   </script><script>
diff --git a/02-placeholders.html b/02-placeholders.html
index 86c89c2..f6b9991 100644
--- a/02-placeholders.html
+++ b/02-placeholders.html
@@ -534,7 +534,7 @@ <h3 class="callout-title">Running the general-purpose rule</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>After editing the file, run the commands:</p>
 <div class="codewrapper sourceCode" id="cb3">
@@ -574,7 +574,7 @@ <h3 class="callout-title">Choosing the right wildcards</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <p>In all cases, there is no need to change the <code>shell</code> part
 of the rule at all.</p>
@@ -702,7 +702,7 @@ <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">
 <pre class="source"><code># Trim any FASTQ reads for base quality
 rule trimreads:
@@ -817,7 +817,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/02-placeholders.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-10-07",
-  "datePublished": "2024-12-17"
+  "datePublished": "2024-12-24"
 }
 
   </script><script>
diff --git a/03-chaining_rules.html b/03-chaining_rules.html
index b818a67..e0b1474 100644
--- a/03-chaining_rules.html
+++ b/03-chaining_rules.html
@@ -537,7 +537,7 @@ <h3 class="callout-title">How many reads were removed?</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>After generating both the trimmed and untrimmed <code>.count</code>
 files we can get this information.</p>
@@ -615,7 +615,7 @@ <h3 class="callout-title">Making this rule generic</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <pre class="source"><code>rule calculate_difference:
     output: "{myfile}.reads_removed.txt"
@@ -742,7 +742,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/03-chaining_rules.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-10-10",
-  "datePublished": "2024-12-17"
+  "datePublished": "2024-12-24"
 }
 
   </script><script>
diff --git a/04-logs_and_errors.html b/04-logs_and_errors.html
index cec04f5..f6ee605 100644
--- a/04-logs_and_errors.html
+++ b/04-logs_and_errors.html
@@ -887,7 +887,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/04-logs_and_errors.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-10-11",
-  "datePublished": "2024-12-17"
+  "datePublished": "2024-12-24"
 }
 
   </script><script>
diff --git a/05-the_dag.html b/05-the_dag.html
index f8d7bb3..b93626d 100644
--- a/05-the_dag.html
+++ b/05-the_dag.html
@@ -492,7 +492,7 @@ <h3 class="callout-title">How many jobs?</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>10 in total: 3 * kallisto_quant // 6 * trimreads // 1 *
 kallisto_index // 0 * countreads</p>
@@ -695,7 +695,7 @@ <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">
@@ -834,7 +834,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/05-the_dag.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-10-10",
-  "datePublished": "2024-12-17"
+  "datePublished": "2024-12-24"
 }
 
   </script><script>
diff --git a/06-expansion.html b/06-expansion.html
index 4dd2469..a8f8831 100644
--- a/06-expansion.html
+++ b/06-expansion.html
@@ -959,7 +959,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/06-expansion.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-10-10",
-  "datePublished": "2024-12-17"
+  "datePublished": "2024-12-24"
 }
 
   </script><script>
diff --git a/07-awkward_programs.html b/07-awkward_programs.html
index e72ed11..90ef88d 100644
--- a/07-awkward_programs.html
+++ b/07-awkward_programs.html
@@ -861,7 +861,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/07-awkward_programs.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-10-07",
-  "datePublished": "2024-12-17"
+  "datePublished": "2024-12-24"
 }
 
   </script><script>
diff --git a/08-finished-workflow.html b/08-finished-workflow.html
index 1d3cab7..01c931f 100644
--- a/08-finished-workflow.html
+++ b/08-finished-workflow.html
@@ -852,7 +852,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/08-finished-workflow.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-10-07",
-  "datePublished": "2024-12-17"
+  "datePublished": "2024-12-24"
 }
 
   </script><script>
diff --git a/09-configuring.html b/09-configuring.html
index f025254..c3a1b17 100644
--- a/09-configuring.html
+++ b/09-configuring.html
@@ -474,7 +474,7 @@ <h3 class="callout-title">Adding a parameter to the
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <pre class="source"><code>rule salmon_index:
     output:
@@ -573,7 +573,7 @@ <h3 class="callout-title">Making the parameter of a rule configurable</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" 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>Rule is as before, aside from:</p>
 <pre class="source"><code><span><span class="va">params</span><span class="op">:</span></span>
@@ -646,7 +646,7 @@ <h3 class="callout-title">Making the conditions and replicates into configurable
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" 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>In <em>config.yaml</em> add the lines:</p>
 <pre class="source"><code>conditions: ["etoh60", "temp33", "ref"]
@@ -758,7 +758,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/09-configuring.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-10-07",
-  "datePublished": "2024-12-17"
+  "datePublished": "2024-12-24"
 }
 
   </script><script>
diff --git a/10-performance.html b/10-performance.html
index 9a26c38..e380530 100644
--- a/10-performance.html
+++ b/10-performance.html
@@ -735,7 +735,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/10-performance.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-10-07",
-  "datePublished": "2024-12-17"
+  "datePublished": "2024-12-24"
 }
 
   </script><script>
diff --git a/11-conda_integration.html b/11-conda_integration.html
index 9601de0..e02692e 100644
--- a/11-conda_integration.html
+++ b/11-conda_integration.html
@@ -844,7 +844,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/11-conda_integration.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-10-10",
-  "datePublished": "2024-12-17"
+  "datePublished": "2024-12-24"
 }
 
   </script><script>
diff --git a/12-assembly_challenge.html b/12-assembly_challenge.html
index ffb4a75..76660da 100644
--- a/12-assembly_challenge.html
+++ b/12-assembly_challenge.html
@@ -734,7 +734,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/12-assembly_challenge.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-10-07",
-  "datePublished": "2024-12-17"
+  "datePublished": "2024-12-24"
 }
 
   </script><script>
diff --git a/13-cleaning_up.html b/13-cleaning_up.html
index 9b25d52..23b3dec 100644
--- a/13-cleaning_up.html
+++ b/13-cleaning_up.html
@@ -532,7 +532,7 @@ <h3 class="callout-title">Removing the HTML reports from FastQC</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>Amend the <em>html</em> output of the <em>fastqc</em> rule to mark it
 as <code>temporary()</code>:</p>
@@ -668,7 +668,7 @@ <h3 class="callout-title">Removing the HTML reports (again)</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <p>The <code>shadow: "minimal"</code> directive will do the job nicely.
 You also need to remove mention of the <code>.html</code> file from the
@@ -768,7 +768,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/13-cleaning_up.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-10-07",
-  "datePublished": "2024-12-17"
+  "datePublished": "2024-12-24"
 }
 
   </script><script>
diff --git a/404.html b/404.html
index 7bc79de..37d84b6 100644
--- a/404.html
+++ b/404.html
@@ -455,8 +455,8 @@ <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": "2024-12-17",
-  "datePublished": "2024-12-17"
+  "dateModified": "2024-12-24",
+  "datePublished": "2024-12-24"
 }
 
   </script><script>
diff --git a/B1-quoting.html b/B1-quoting.html
index b9be69c..7530f5a 100644
--- a/B1-quoting.html
+++ b/B1-quoting.html
@@ -720,7 +720,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/B1-quoting.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-10-07",
-  "datePublished": "2024-12-17"
+  "datePublished": "2024-12-24"
 }
 
   </script><script>
diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html
index 713b162..cd5ce66 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": "2024-12-17"
+  "datePublished": "2024-12-24"
 }
 
   </script><script>
diff --git a/LICENSE.html b/LICENSE.html
index 7d3eb2f..6272446 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -561,7 +561,7 @@ <h3 id="yeast-transcriptome">Yeast transcriptome<a class="anchor" aria-label="an
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/LICENSE.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-02-22",
-  "datePublished": "2024-12-17"
+  "datePublished": "2024-12-24"
 }
 
   </script><script>
diff --git a/aio.html b/aio.html
index ed23ac4..9dc0225 100644
--- a/aio.html
+++ b/aio.html
@@ -931,7 +931,7 @@ <h3 class="callout-title">Running the general-purpose rule</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>After editing the file, run the commands:</p>
 <div class="codewrapper sourceCode" id="cb3">
@@ -973,7 +973,7 @@ <h3 class="callout-title">Choosing the right wildcards</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <p>In all cases, there is no need to change the <code>shell</code> part
 of the rule at all.</p>
@@ -1118,7 +1118,7 @@ <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">
 <pre class="source"><code># Trim any FASTQ reads for base quality
 rule trimreads:
@@ -1333,7 +1333,7 @@ <h3 class="callout-title">How many reads were removed?</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>After generating both the trimmed and untrimmed <code>.count</code>
 files we can get this information.</p>
@@ -1413,7 +1413,7 @@ <h3 class="callout-title">Making this rule generic</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <pre class="source"><code>rule calculate_difference:
     output: "{myfile}.reads_removed.txt"
@@ -2043,7 +2043,7 @@ <h3 class="callout-title">How many jobs?</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>10 in total: 3 * kallisto_quant // 6 * trimreads // 1 *
 kallisto_index // 0 * countreads</p>
@@ -2258,7 +2258,7 @@ <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">
@@ -3801,7 +3801,7 @@ <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" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <pre class="source"><code>rule salmon_index:
     output:
@@ -3904,7 +3904,7 @@ <h3 class="callout-title">Making the parameter of a rule configurable</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" 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>Rule is as before, aside from:</p>
 <pre class="source"><code><span><span class="va">params</span><span class="op">:</span></span>
@@ -3981,7 +3981,7 @@ <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" 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>In <em>config.yaml</em> add the lines:</p>
 <pre class="source"><code>conditions: ["etoh60", "temp33", "ref"]
@@ -5226,7 +5226,7 @@ <h3 class="callout-title">Removing the HTML reports from FastQC</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>Amend the <em>html</em> output of the <em>fastqc</em> rule to mark it
 as <code>temporary()</code>:</p>
@@ -5370,7 +5370,7 @@ <h3 class="callout-title">Removing the HTML reports (again)</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <p>The <code>shadow: "minimal"</code> directive will do the job nicely.
 You also need to remove mention of the <code>.html</code> file from the
@@ -5461,8 +5461,8 @@ <h3 class="callout-title">Key Points</h3>
   "url": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/aio.html",
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/aio.html",
   "dateCreated": "2021-03-26",
-  "dateModified": "2024-12-17",
-  "datePublished": "2024-12-17"
+  "dateModified": "2024-12-24",
+  "datePublished": "2024-12-24"
 }
 
   </script><script>
diff --git a/discuss.html b/discuss.html
index f570045..87ba140 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": "2024-12-17"
+  "datePublished": "2024-12-24"
 }
 
   </script><script>
diff --git a/images.html b/images.html
index 1597e1b..7c8e4ef 100644
--- a/images.html
+++ b/images.html
@@ -541,8 +541,8 @@ <h3 id="12-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": "2024-12-17",
-  "datePublished": "2024-12-17"
+  "dateModified": "2024-12-24",
+  "datePublished": "2024-12-24"
 }
 
   </script><script>
diff --git a/index.html b/index.html
index 8509e5e..f54da2e 100644
--- a/index.html
+++ b/index.html
@@ -645,8 +645,8 @@ <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": "2024-12-17",
-  "datePublished": "2024-12-17"
+  "dateModified": "2024-12-24",
+  "datePublished": "2024-12-24"
 }
 
   </script><script>
diff --git a/instructor-notes.html b/instructor-notes.html
index e9c72c0..12a5e3d 100644
--- a/instructor-notes.html
+++ b/instructor-notes.html
@@ -599,8 +599,8 @@ <h3 id="q-example-question-here">Q: Example question here?<a class="anchor" aria
   "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": "2024-12-17",
-  "datePublished": "2024-12-17"
+  "dateModified": "2024-12-24",
+  "datePublished": "2024-12-24"
 }
 
   </script><script>
diff --git a/instructor/01-introduction.html b/instructor/01-introduction.html
index 5b1223e..25d9512 100644
--- a/instructor/01-introduction.html
+++ b/instructor/01-introduction.html
@@ -797,7 +797,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/01-introduction.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-10-07",
-  "datePublished": "2024-12-17"
+  "datePublished": "2024-12-24"
 }
 
   </script><script>
diff --git a/instructor/02-placeholders.html b/instructor/02-placeholders.html
index 799a449..bd7666b 100644
--- a/instructor/02-placeholders.html
+++ b/instructor/02-placeholders.html
@@ -536,7 +536,7 @@ <h3 class="callout-title">Running the general-purpose rule</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>After editing the file, run the commands:</p>
 <div class="codewrapper sourceCode" id="cb3">
@@ -576,7 +576,7 @@ <h3 class="callout-title">Choosing the right wildcards</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <p>In all cases, there is no need to change the <code>shell</code> part
 of the rule at all.</p>
@@ -704,7 +704,7 @@ <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">
 <pre class="source"><code># Trim any FASTQ reads for base quality
 rule trimreads:
@@ -819,7 +819,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/02-placeholders.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-10-07",
-  "datePublished": "2024-12-17"
+  "datePublished": "2024-12-24"
 }
 
   </script><script>
diff --git a/instructor/03-chaining_rules.html b/instructor/03-chaining_rules.html
index 17d4dc6..5da7d28 100644
--- a/instructor/03-chaining_rules.html
+++ b/instructor/03-chaining_rules.html
@@ -501,7 +501,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <button class="accordion-button instructor-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseInstructor1" aria-expanded="false" aria-controls="collapseInstructor1">
   <h3 class="accordion-header" id="headingInstructor1">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="edit-2"></i></div> Illustrating the wildcard matching process </h3>
 </button>
-<div id="collapseInstructor1" class="accordion-collapse collapse" aria-labelledby="headingInstructor1" data-bs-parent="#accordionInstructor1">
+<div id="collapseInstructor1" class="accordion-collapse collapse" data-bs-parent="#accordionInstructor1" aria-labelledby="headingInstructor1">
 <div class="accordion-body">
 <p>A figure is shown here to illustrate the way Snakemake finds rules by
 wildcard matching and then tracks back until it runs out of rule matches
@@ -555,7 +555,7 @@ <h3 class="callout-title">How many reads were removed?</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>After generating both the trimmed and untrimmed <code>.count</code>
 files we can get this information.</p>
@@ -633,7 +633,7 @@ <h3 class="callout-title">Making this rule generic</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <pre class="source"><code>rule calculate_difference:
     output: "{myfile}.reads_removed.txt"
@@ -760,7 +760,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/03-chaining_rules.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-10-10",
-  "datePublished": "2024-12-17"
+  "datePublished": "2024-12-24"
 }
 
   </script><script>
diff --git a/instructor/04-logs_and_errors.html b/instructor/04-logs_and_errors.html
index 3ecb3ba..97e275f 100644
--- a/instructor/04-logs_and_errors.html
+++ b/instructor/04-logs_and_errors.html
@@ -912,7 +912,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/04-logs_and_errors.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-10-11",
-  "datePublished": "2024-12-17"
+  "datePublished": "2024-12-24"
 }
 
   </script><script>
diff --git a/instructor/05-the_dag.html b/instructor/05-the_dag.html
index 724f59f..4d53e67 100644
--- a/instructor/05-the_dag.html
+++ b/instructor/05-the_dag.html
@@ -494,7 +494,7 @@ <h3 class="callout-title">How many jobs?</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>10 in total: 3 * kallisto_quant // 6 * trimreads // 1 *
 kallisto_index // 0 * countreads</p>
@@ -697,7 +697,7 @@ <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">
@@ -836,7 +836,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/05-the_dag.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-10-10",
-  "datePublished": "2024-12-17"
+  "datePublished": "2024-12-24"
 }
 
   </script><script>
diff --git a/instructor/06-expansion.html b/instructor/06-expansion.html
index 34e41b8..01041a6 100644
--- a/instructor/06-expansion.html
+++ b/instructor/06-expansion.html
@@ -961,7 +961,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/06-expansion.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-10-10",
-  "datePublished": "2024-12-17"
+  "datePublished": "2024-12-24"
 }
 
   </script><script>
diff --git a/instructor/07-awkward_programs.html b/instructor/07-awkward_programs.html
index 52df911..22fec2a 100644
--- a/instructor/07-awkward_programs.html
+++ b/instructor/07-awkward_programs.html
@@ -863,7 +863,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/07-awkward_programs.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-10-07",
-  "datePublished": "2024-12-17"
+  "datePublished": "2024-12-24"
 }
 
   </script><script>
diff --git a/instructor/08-finished-workflow.html b/instructor/08-finished-workflow.html
index a2f0d62..4db0c57 100644
--- a/instructor/08-finished-workflow.html
+++ b/instructor/08-finished-workflow.html
@@ -871,7 +871,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/08-finished-workflow.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-10-07",
-  "datePublished": "2024-12-17"
+  "datePublished": "2024-12-24"
 }
 
   </script><script>
diff --git a/instructor/09-configuring.html b/instructor/09-configuring.html
index 36f5216..6e6d586 100644
--- a/instructor/09-configuring.html
+++ b/instructor/09-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" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <pre class="source"><code>rule salmon_index:
     output:
@@ -575,7 +575,7 @@ <h3 class="callout-title">Making the parameter of a rule configurable</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" 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>Rule is as before, aside from:</p>
 <pre class="source"><code><span><span class="va">params</span><span class="op">:</span></span>
@@ -648,7 +648,7 @@ <h3 class="callout-title">Making the conditions and replicates into configurable
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" 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>In <em>config.yaml</em> add the lines:</p>
 <pre class="source"><code>conditions: ["etoh60", "temp33", "ref"]
@@ -760,7 +760,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/09-configuring.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-10-07",
-  "datePublished": "2024-12-17"
+  "datePublished": "2024-12-24"
 }
 
   </script><script>
diff --git a/instructor/10-performance.html b/instructor/10-performance.html
index 65ccb3d..8acdea4 100644
--- a/instructor/10-performance.html
+++ b/instructor/10-performance.html
@@ -761,7 +761,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/10-performance.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-10-07",
-  "datePublished": "2024-12-17"
+  "datePublished": "2024-12-24"
 }
 
   </script><script>
diff --git a/instructor/11-conda_integration.html b/instructor/11-conda_integration.html
index e0dad4b..4aefe6f 100644
--- a/instructor/11-conda_integration.html
+++ b/instructor/11-conda_integration.html
@@ -846,7 +846,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/11-conda_integration.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-10-10",
-  "datePublished": "2024-12-17"
+  "datePublished": "2024-12-24"
 }
 
   </script><script>
diff --git a/instructor/12-assembly_challenge.html b/instructor/12-assembly_challenge.html
index 73c3efd..d06a199 100644
--- a/instructor/12-assembly_challenge.html
+++ b/instructor/12-assembly_challenge.html
@@ -736,7 +736,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/12-assembly_challenge.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-10-07",
-  "datePublished": "2024-12-17"
+  "datePublished": "2024-12-24"
 }
 
   </script><script>
diff --git a/instructor/13-cleaning_up.html b/instructor/13-cleaning_up.html
index 20707c1..aa0c481 100644
--- a/instructor/13-cleaning_up.html
+++ b/instructor/13-cleaning_up.html
@@ -534,7 +534,7 @@ <h3 class="callout-title">Removing the HTML reports from FastQC</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>Amend the <em>html</em> output of the <em>fastqc</em> rule to mark it
 as <code>temporary()</code>:</p>
@@ -670,7 +670,7 @@ <h3 class="callout-title">Removing the HTML reports (again)</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <p>The <code>shadow: "minimal"</code> directive will do the job nicely.
 You also need to remove mention of the <code>.html</code> file from the
@@ -770,7 +770,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/13-cleaning_up.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-10-07",
-  "datePublished": "2024-12-17"
+  "datePublished": "2024-12-24"
 }
 
   </script><script>
diff --git a/instructor/404.html b/instructor/404.html
index 9bcf9c9..5504c7a 100644
--- a/instructor/404.html
+++ b/instructor/404.html
@@ -455,8 +455,8 @@ <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": "2024-12-17",
-  "datePublished": "2024-12-17"
+  "dateModified": "2024-12-24",
+  "datePublished": "2024-12-24"
 }
 
   </script><script>
diff --git a/instructor/B1-quoting.html b/instructor/B1-quoting.html
index ce287ac..6371964 100644
--- a/instructor/B1-quoting.html
+++ b/instructor/B1-quoting.html
@@ -722,7 +722,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/B1-quoting.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-10-07",
-  "datePublished": "2024-12-17"
+  "datePublished": "2024-12-24"
 }
 
   </script><script>
diff --git a/instructor/CODE_OF_CONDUCT.html b/instructor/CODE_OF_CONDUCT.html
index d6a9d9b..8279859 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": "2024-12-17"
+  "datePublished": "2024-12-24"
 }
 
   </script><script>
diff --git a/instructor/LICENSE.html b/instructor/LICENSE.html
index 6d7e691..8d61af4 100644
--- a/instructor/LICENSE.html
+++ b/instructor/LICENSE.html
@@ -563,7 +563,7 @@ <h3 id="yeast-transcriptome">Yeast transcriptome<a class="anchor" aria-label="an
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/LICENSE.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-02-22",
-  "datePublished": "2024-12-17"
+  "datePublished": "2024-12-24"
 }
 
   </script><script>
diff --git a/instructor/aio.html b/instructor/aio.html
index 4d482fd..e3f6c0e 100644
--- a/instructor/aio.html
+++ b/instructor/aio.html
@@ -975,7 +975,7 @@ <h3 class="callout-title">Running the general-purpose rule</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>After editing the file, run the commands:</p>
 <div class="codewrapper sourceCode" id="cb3">
@@ -1017,7 +1017,7 @@ <h3 class="callout-title">Choosing the right wildcards</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <p>In all cases, there is no need to change the <code>shell</code> part
 of the rule at all.</p>
@@ -1162,7 +1162,7 @@ <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">
 <pre class="source"><code># Trim any FASTQ reads for base quality
 rule trimreads:
@@ -1336,7 +1336,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <button class="accordion-button instructor-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseInstructor1" aria-expanded="false" aria-controls="collapseInstructor1">
   <h3 class="accordion-header" id="headingInstructor1">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="edit-2"></i></div> Illustrating the wildcard matching process </h3>
 </button>
-<div id="collapseInstructor1" class="accordion-collapse collapse" aria-labelledby="headingInstructor1" data-bs-parent="#accordionInstructor1">
+<div id="collapseInstructor1" class="accordion-collapse collapse" data-bs-parent="#accordionInstructor1" aria-labelledby="headingInstructor1">
 <div class="accordion-body">
 <p>A figure is shown here to illustrate the way Snakemake finds rules by
 wildcard matching and then tracks back until it runs out of rule matches
@@ -1394,7 +1394,7 @@ <h3 class="callout-title">How many reads were removed?</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>After generating both the trimmed and untrimmed <code>.count</code>
 files we can get this information.</p>
@@ -1474,7 +1474,7 @@ <h3 class="callout-title">Making this rule generic</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <pre class="source"><code>rule calculate_difference:
     output: "{myfile}.reads_removed.txt"
@@ -2129,7 +2129,7 @@ <h3 class="callout-title">How many jobs?</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>10 in total: 3 * kallisto_quant // 6 * trimreads // 1 *
 kallisto_index // 0 * countreads</p>
@@ -2344,7 +2344,7 @@ <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">
@@ -3908,7 +3908,7 @@ <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" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <pre class="source"><code>rule salmon_index:
     output:
@@ -4011,7 +4011,7 @@ <h3 class="callout-title">Making the parameter of a rule configurable</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" 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>Rule is as before, aside from:</p>
 <pre class="source"><code><span><span class="va">params</span><span class="op">:</span></span>
@@ -4088,7 +4088,7 @@ <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" 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>In <em>config.yaml</em> add the lines:</p>
 <pre class="source"><code>conditions: ["etoh60", "temp33", "ref"]
@@ -5361,7 +5361,7 @@ <h3 class="callout-title">Removing the HTML reports from FastQC</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>Amend the <em>html</em> output of the <em>fastqc</em> rule to mark it
 as <code>temporary()</code>:</p>
@@ -5505,7 +5505,7 @@ <h3 class="callout-title">Removing the HTML reports (again)</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <p>The <code>shadow: "minimal"</code> directive will do the job nicely.
 You also need to remove mention of the <code>.html</code> file from the
@@ -5596,8 +5596,8 @@ <h3 class="callout-title">Key Points</h3>
   "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": "2024-12-17",
-  "datePublished": "2024-12-17"
+  "dateModified": "2024-12-24",
+  "datePublished": "2024-12-24"
 }
 
   </script><script>
diff --git a/instructor/discuss.html b/instructor/discuss.html
index 250978b..a3e0688 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": "2024-12-17"
+  "datePublished": "2024-12-24"
 }
 
   </script><script>
diff --git a/instructor/images.html b/instructor/images.html
index 9fc102e..c45c802 100644
--- a/instructor/images.html
+++ b/instructor/images.html
@@ -543,8 +543,8 @@ <h3 id="12-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": "2024-12-17",
-  "datePublished": "2024-12-17"
+  "dateModified": "2024-12-24",
+  "datePublished": "2024-12-24"
 }
 
   </script><script>
diff --git a/instructor/index.html b/instructor/index.html
index f428280..45ba3d6 100644
--- a/instructor/index.html
+++ b/instructor/index.html
@@ -781,8 +781,8 @@ <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": "2024-12-17",
-  "datePublished": "2024-12-17"
+  "dateModified": "2024-12-24",
+  "datePublished": "2024-12-24"
 }
 
   </script><script>
diff --git a/instructor/instructor-notes.html b/instructor/instructor-notes.html
index d69f6bd..c7a67dc 100644
--- a/instructor/instructor-notes.html
+++ b/instructor/instructor-notes.html
@@ -701,8 +701,8 @@ <h3 id="10-performance-headingInstructor1">
   "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": "2024-12-17",
-  "datePublished": "2024-12-17"
+  "dateModified": "2024-12-24",
+  "datePublished": "2024-12-24"
 }
 
   </script><script>
diff --git a/instructor/key-points.html b/instructor/key-points.html
index c5c3d12..e55cca7 100644
--- a/instructor/key-points.html
+++ b/instructor/key-points.html
@@ -639,8 +639,8 @@ <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": "2024-12-17",
-  "datePublished": "2024-12-17"
+  "dateModified": "2024-12-24",
+  "datePublished": "2024-12-24"
 }
 
   </script><script>
diff --git a/instructor/paper.html b/instructor/paper.html
index 75932b5..3106827 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": "2024-12-17"
+  "datePublished": "2024-12-24"
 }
 
   </script><script>
diff --git a/instructor/prereqs.html b/instructor/prereqs.html
index 4765121..261cabb 100644
--- a/instructor/prereqs.html
+++ b/instructor/prereqs.html
@@ -574,7 +574,7 @@ <h3 id="shell-syntax-and-common-commands">Shell syntax and common commands<a cla
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/prereqs.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-10-07",
-  "datePublished": "2024-12-17"
+  "datePublished": "2024-12-24"
 }
 
   </script><script>
diff --git a/instructor/profiles.html b/instructor/profiles.html
index 89b8496..4f4940a 100644
--- a/instructor/profiles.html
+++ b/instructor/profiles.html
@@ -479,8 +479,8 @@ <h1>Learner Profiles</h1>
   "url": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/profiles.html",
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/profiles.html",
   "dateCreated": "2021-03-26",
-  "dateModified": "2024-12-17",
-  "datePublished": "2024-12-17"
+  "dateModified": "2024-12-24",
+  "datePublished": "2024-12-24"
 }
 
   </script><script>
diff --git a/instructor/reference.html b/instructor/reference.html
index 2b8c144..b33b8c6 100644
--- a/instructor/reference.html
+++ b/instructor/reference.html
@@ -498,7 +498,7 @@ <h1>Reference</h1>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/instructor/reference.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-10-07",
-  "datePublished": "2024-12-17"
+  "datePublished": "2024-12-24"
 }
 
   </script><script>
diff --git a/key-points.html b/key-points.html
index 3aff3a2..75accb1 100644
--- a/key-points.html
+++ b/key-points.html
@@ -637,8 +637,8 @@ <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": "2024-12-17",
-  "datePublished": "2024-12-17"
+  "dateModified": "2024-12-24",
+  "datePublished": "2024-12-24"
 }
 
   </script><script>
diff --git a/paper.html b/paper.html
index 7627de3..42506ae 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": "2024-12-17"
+  "datePublished": "2024-12-24"
 }
 
   </script><script>
diff --git a/pkgdown.yml b/pkgdown.yml
index 6031b98..4c4183f 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,4 +2,4 @@ pandoc: 3.1.11
 pkgdown: 2.1.1
 pkgdown_sha: ~
 articles: {}
-last_built: 2024-12-17T01:06Z
+last_built: 2024-12-24T01:00Z
diff --git a/prereqs.html b/prereqs.html
index 920640b..f679d9f 100644
--- a/prereqs.html
+++ b/prereqs.html
@@ -572,7 +572,7 @@ <h3 id="shell-syntax-and-common-commands">Shell syntax and common commands<a cla
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/prereqs.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-10-07",
-  "datePublished": "2024-12-17"
+  "datePublished": "2024-12-24"
 }
 
   </script><script>
diff --git a/profiles.html b/profiles.html
index de9af1a..0aa3775 100644
--- a/profiles.html
+++ b/profiles.html
@@ -479,8 +479,8 @@ <h1>Learner Profiles</h1>
   "url": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/profiles.html",
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/profiles.html",
   "dateCreated": "2021-03-26",
-  "dateModified": "2024-12-17",
-  "datePublished": "2024-12-17"
+  "dateModified": "2024-12-24",
+  "datePublished": "2024-12-24"
 }
 
   </script><script>
diff --git a/reference.html b/reference.html
index 505a148..dacd927 100644
--- a/reference.html
+++ b/reference.html
@@ -496,7 +496,7 @@ <h1>Reference</h1>
   "identifier": "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/reference.html",
   "dateCreated": "2021-03-26",
   "dateModified": "2024-10-07",
-  "datePublished": "2024-12-17"
+  "datePublished": "2024-12-24"
 }
 
   </script><script>