From c82bdbb6af263906fcce4b045dedcda7357f10dd Mon Sep 17 00:00:00 2001
From: GitHub Actions <actions@github.com>
Date: Tue, 29 Oct 2024 01:02:37 +0000
Subject: [PATCH] site deploy

Auto-generated via `{sandpaper}`
Source  : f708efbc5b4492a16dca1c1909598b5d8a22134e
Branch  : md-outputs
Author  : GitHub Actions <actions@github.com>
Time    : 2024-09-27 08:49:48 +0000
Message : markdown source builds

Auto-generated via {sandpaper}
Source  : 91ca9aab991bbb893f3c6e14b5084d3ba4d945d2
Branch  : main
Author  : Graeme Grimes <graeme.grimes@ed.ac.uk>
Time    : 2024-09-27 08:48:41 +0000
Message : Merge pull request #170 from chiasinL/patch-1

Fix input qualifier for the QUANT step and minor typo in the page
---
 01-getting-started-with-nextflow.html         |  2 +-
 02-workflow_parameters.html                   |  2 +-
 03-channels.html                              |  2 +-
 04-processes-part1.html                       |  2 +-
 05-processes-part2.html                       |  2 +-
 06-workflow.html                              |  2 +-
 07-operators.html                             |  2 +-
 08-reporting.html                             | 10 +++---
 09-configuration.html                         |  2 +-
 10-workflow_checkpoint_caching.html           |  8 ++---
 11-Simple_Rna-Seq_pipeline.html               | 20 +++++------
 12-nfcore.html                                |  2 +-
 404.html                                      |  4 +--
 CODE_OF_CONDUCT.html                          |  2 +-
 LICENSE.html                                  |  2 +-
 aio.html                                      | 36 +++++++++----------
 discuss.html                                  |  2 +-
 images.html                                   |  4 +--
 index.html                                    |  4 +--
 instructor-notes.html                         |  4 +--
 .../01-getting-started-with-nextflow.html     |  2 +-
 instructor/02-workflow_parameters.html        |  2 +-
 instructor/03-channels.html                   |  2 +-
 instructor/04-processes-part1.html            |  2 +-
 instructor/05-processes-part2.html            |  2 +-
 instructor/06-workflow.html                   |  2 +-
 instructor/07-operators.html                  |  2 +-
 instructor/08-reporting.html                  | 10 +++---
 instructor/09-configuration.html              |  2 +-
 .../10-workflow_checkpoint_caching.html       |  8 ++---
 instructor/11-Simple_Rna-Seq_pipeline.html    | 20 +++++------
 instructor/12-nfcore.html                     |  2 +-
 instructor/404.html                           |  4 +--
 instructor/CODE_OF_CONDUCT.html               |  2 +-
 instructor/LICENSE.html                       |  2 +-
 instructor/aio.html                           | 36 +++++++++----------
 instructor/discuss.html                       |  2 +-
 instructor/images.html                        |  4 +--
 instructor/index.html                         |  4 +--
 instructor/instructor-notes.html              |  4 +--
 instructor/key-points.html                    |  4 +--
 instructor/learner_profiles.html              |  2 +-
 instructor/profiles.html                      |  4 +--
 instructor/reference.html                     |  2 +-
 key-points.html                               |  4 +--
 learner_profiles.html                         |  2 +-
 pkgdown.yml                                   |  2 +-
 profiles.html                                 |  4 +--
 reference.html                                |  2 +-
 49 files changed, 127 insertions(+), 127 deletions(-)

diff --git a/01-getting-started-with-nextflow.html b/01-getting-started-with-nextflow.html
index 5489e801..cfad5bf1 100644
--- a/01-getting-started-with-nextflow.html
+++ b/01-getting-started-with-nextflow.html
@@ -776,7 +776,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/workflows-nextflow/01-getting-started-with-nextflow.html",
   "dateCreated": "2021-02-01",
   "dateModified": "2024-06-10",
-  "datePublished": "2024-10-22"
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/02-workflow_parameters.html b/02-workflow_parameters.html
index 575cc642..91438bad 100644
--- a/02-workflow_parameters.html
+++ b/02-workflow_parameters.html
@@ -803,7 +803,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/workflows-nextflow/02-workflow_parameters.html",
   "dateCreated": "2021-02-01",
   "dateModified": "2024-08-23",
-  "datePublished": "2024-10-22"
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/03-channels.html b/03-channels.html
index 8afe015a..e5749291 100644
--- a/03-channels.html
+++ b/03-channels.html
@@ -1182,7 +1182,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/workflows-nextflow/03-channels.html",
   "dateCreated": "2021-02-01",
   "dateModified": "2024-08-23",
-  "datePublished": "2024-10-22"
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/04-processes-part1.html b/04-processes-part1.html
index 0c1f2a81..236d9e27 100644
--- a/04-processes-part1.html
+++ b/04-processes-part1.html
@@ -2017,7 +2017,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/workflows-nextflow/04-processes-part1.html",
   "dateCreated": "2021-02-01",
   "dateModified": "2024-08-23",
-  "datePublished": "2024-10-22"
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/05-processes-part2.html b/05-processes-part2.html
index e2fd21e9..f25df57e 100644
--- a/05-processes-part2.html
+++ b/05-processes-part2.html
@@ -1504,7 +1504,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/workflows-nextflow/05-processes-part2.html",
   "dateCreated": "2021-02-01",
   "dateModified": "2024-06-10",
-  "datePublished": "2024-10-22"
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/06-workflow.html b/06-workflow.html
index 5fc957ed..f0f906e4 100644
--- a/06-workflow.html
+++ b/06-workflow.html
@@ -814,7 +814,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/workflows-nextflow/06-workflow.html",
   "dateCreated": "2021-02-01",
   "dateModified": "2024-06-10",
-  "datePublished": "2024-10-22"
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/07-operators.html b/07-operators.html
index fedcca44..1b1d4002 100644
--- a/07-operators.html
+++ b/07-operators.html
@@ -1381,7 +1381,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/workflows-nextflow/07-operators.html",
   "dateCreated": "2021-02-01",
   "dateModified": "2024-04-23",
-  "datePublished": "2024-10-22"
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/08-reporting.html b/08-reporting.html
index a21a1a70..8e72ecd0 100644
--- a/08-reporting.html
+++ b/08-reporting.html
@@ -464,7 +464,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>The output will look similar to this:</p>
 <div class="codewrapper">
@@ -639,7 +639,7 @@ <h3 class="callout-title">View run log</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>Example solution using run name <code>elegant_descartes</code>.</p>
 <div class="codewrapper sourceCode" id="cb13">
@@ -668,7 +668,7 @@ <h3 class="callout-title">Filter pipeline run log</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb14">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -752,7 +752,7 @@ <h3 class="callout-title">Generate an HTML run report</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb19">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -836,7 +836,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/workflows-nextflow/08-reporting.html",
   "dateCreated": "2021-02-01",
   "dateModified": "2024-04-23",
-  "datePublished": "2024-10-22"
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/09-configuration.html b/09-configuration.html
index 4c071e8b..47f161ec 100644
--- a/09-configuration.html
+++ b/09-configuration.html
@@ -1396,7 +1396,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/workflows-nextflow/09-configuration.html",
   "dateCreated": "2021-02-01",
   "dateModified": "2024-06-10",
-  "datePublished": "2024-10-22"
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/10-workflow_checkpoint_caching.html b/10-workflow_checkpoint_caching.html
index 89e97ffe..32400651 100644
--- a/10-workflow_checkpoint_caching.html
+++ b/10-workflow_checkpoint_caching.html
@@ -468,7 +468,7 @@ <h3 class="callout-title">Resume a pipeline</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" 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">
 <div class="codewrapper sourceCode" id="cb3">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -568,7 +568,7 @@ <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>The output will look similar to this:</p>
 <div class="codewrapper">
@@ -780,7 +780,7 @@ <h3 class="callout-title">Remove a Nextflow run.</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <p>An example nextflow clean command with <code>dry-run</code> .</p>
 <div class="codewrapper sourceCode" id="cb14">
@@ -876,7 +876,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/workflows-nextflow/10-workflow_checkpoint_caching.html",
   "dateCreated": "2021-02-01",
   "dateModified": "2024-08-21",
-  "datePublished": "2024-10-22"
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/11-Simple_Rna-Seq_pipeline.html b/11-Simple_Rna-Seq_pipeline.html
index 79aae4c9..21df0708 100644
--- a/11-Simple_Rna-Seq_pipeline.html
+++ b/11-Simple_Rna-Seq_pipeline.html
@@ -546,7 +546,7 @@ <h3 class="callout-title">Add a parameter</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">
 <div class="codewrapper sourceCode" id="cb10">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -595,7 +595,7 @@ <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" 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>Below is an example log.info command printing all the pipeline
 parameters.</p>
@@ -779,7 +779,7 @@ <h3 class="callout-title">View the contents of the index_ch</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb22">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -926,7 +926,7 @@ <h3 class="callout-title">Read in all read pairs</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb32">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1069,7 +1069,7 @@ <h3 class="callout-title">Add a tag directive</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
   <h4 class="accordion-header" id="headingSolution5"> Show me the solution </h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb40">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1111,7 +1111,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution6" aria-expanded="false" aria-controls="collapseSolution6">
   <h4 class="accordion-header" id="headingSolution6"> Show me the solution </h4>
 </button>
-<div id="collapseSolution6" class="accordion-collapse collapse" aria-labelledby="headingSolution6" data-bs-parent="#accordionSolution6">
+<div id="collapseSolution6" class="accordion-collapse collapse" data-bs-parent="#accordionSolution6" aria-labelledby="headingSolution6">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb41">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1208,7 +1208,7 @@ <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="#collapseSolution7" aria-expanded="false" aria-controls="collapseSolution7">
   <h4 class="accordion-header" id="headingSolution7"> Show me the solution </h4>
 </button>
-<div id="collapseSolution7" class="accordion-collapse collapse" aria-labelledby="headingSolution7" data-bs-parent="#accordionSolution7">
+<div id="collapseSolution7" class="accordion-collapse collapse" data-bs-parent="#accordionSolution7" aria-labelledby="headingSolution7">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb45">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1292,7 +1292,7 @@ <h3 class="callout-title">Combining operators</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution8" aria-expanded="false" aria-controls="collapseSolution8">
   <h4 class="accordion-header" id="headingSolution8"> Show me the solution </h4>
 </button>
-<div id="collapseSolution8" class="accordion-collapse collapse" aria-labelledby="headingSolution8" data-bs-parent="#accordionSolution8">
+<div id="collapseSolution8" class="accordion-collapse collapse" data-bs-parent="#accordionSolution8" aria-labelledby="headingSolution8">
 <div class="accordion-body">
 <p>You need to use the <code>mix</code> operator first to combine the
 channels followed by the <code>collect</code> operator to collect all
@@ -1452,7 +1452,7 @@ <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="#collapseSolution9" aria-expanded="false" aria-controls="collapseSolution9">
   <h4 class="accordion-header" id="headingSolution9"> Show me the solution </h4>
 </button>
-<div id="collapseSolution9" class="accordion-collapse collapse" aria-labelledby="headingSolution9" data-bs-parent="#accordionSolution9">
+<div id="collapseSolution9" class="accordion-collapse collapse" data-bs-parent="#accordionSolution9" aria-labelledby="headingSolution9">
 <div class="accordion-body">
 <p>The <code>INDEX</code> process should be the longest running process.
 dag.png <img src="fig/dag.png" alt="dag" class="figure"> The vertices in the graph
@@ -1564,7 +1564,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/workflows-nextflow/11-Simple_Rna-Seq_pipeline.html",
   "dateCreated": "2021-02-01",
   "dateModified": "2024-09-27",
-  "datePublished": "2024-10-22"
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/12-nfcore.html b/12-nfcore.html
index 0a591399..74b3c41a 100644
--- a/12-nfcore.html
+++ b/12-nfcore.html
@@ -1346,7 +1346,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/workflows-nextflow/12-nfcore.html",
   "dateCreated": "2021-02-01",
   "dateModified": "2024-07-22",
-  "datePublished": "2024-10-22"
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/404.html b/404.html
index d19c143d..f4cf162b 100644
--- a/404.html
+++ b/404.html
@@ -440,8 +440,8 @@ <h1>Page not found</h1>
   "url": "https://carpentries-incubator.github.io/workflows-nextflow/404.html",
   "identifier": "https://carpentries-incubator.github.io/workflows-nextflow/404.html",
   "dateCreated": "2021-02-01",
-  "dateModified": "2024-10-22",
-  "datePublished": "2024-10-22"
+  "dateModified": "2024-10-29",
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html
index e351cfb8..752b76bb 100644
--- a/CODE_OF_CONDUCT.html
+++ b/CODE_OF_CONDUCT.html
@@ -449,7 +449,7 @@ <h1>Contributor Code of Conduct</h1>
   "identifier": "https://carpentries-incubator.github.io/workflows-nextflow/CODE_OF_CONDUCT.html",
   "dateCreated": "2021-02-01",
   "dateModified": "2023-12-08",
-  "datePublished": "2024-10-22"
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/LICENSE.html b/LICENSE.html
index cfc792ad..27139aba 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -497,7 +497,7 @@ <h1>Licenses</h1>
   "identifier": "https://carpentries-incubator.github.io/workflows-nextflow/LICENSE.html",
   "dateCreated": "2021-02-01",
   "dateModified": "2023-12-08",
-  "datePublished": "2024-10-22"
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/aio.html b/aio.html
index e3a29ab4..075b05eb 100644
--- a/aio.html
+++ b/aio.html
@@ -6139,7 +6139,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>The output will look similar to this:</p>
 <div class="codewrapper">
@@ -6322,7 +6322,7 @@ <h3 class="callout-title">View run log</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>Example solution using run name <code>elegant_descartes</code>.</p>
 <div class="codewrapper sourceCode" id="cb13">
@@ -6351,7 +6351,7 @@ <h3 class="callout-title">Filter pipeline run log</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb14">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -6437,7 +6437,7 @@ <h3 class="callout-title">Generate an HTML run report</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb19">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -7559,7 +7559,7 @@ <h3 class="callout-title">Resume a pipeline</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" 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">
 <div class="codewrapper sourceCode" id="cb3">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -7665,7 +7665,7 @@ <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>The output will look similar to this:</p>
 <div class="codewrapper">
@@ -7884,7 +7884,7 @@ <h3 class="callout-title">Remove a Nextflow run.</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <p>An example nextflow clean command with <code>dry-run</code> .</p>
 <div class="codewrapper sourceCode" id="cb14">
@@ -8091,7 +8091,7 @@ <h3 class="callout-title">Add a parameter</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">
 <div class="codewrapper sourceCode" id="cb10">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -8140,7 +8140,7 @@ <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" 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>Below is an example log.info command printing all the pipeline
 parameters.</p>
@@ -8335,7 +8335,7 @@ <h3 class="callout-title">View the contents of the index_ch</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb22">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -8489,7 +8489,7 @@ <h3 class="callout-title">Read in all read pairs</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb32">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -8639,7 +8639,7 @@ <h3 class="callout-title">Add a tag directive</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
   <h4 class="accordion-header" id="headingSolution5"> Show me the solution </h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb40">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -8683,7 +8683,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution6" aria-expanded="false" aria-controls="collapseSolution6">
   <h4 class="accordion-header" id="headingSolution6"> Show me the solution </h4>
 </button>
-<div id="collapseSolution6" class="accordion-collapse collapse" aria-labelledby="headingSolution6" data-bs-parent="#accordionSolution6">
+<div id="collapseSolution6" class="accordion-collapse collapse" data-bs-parent="#accordionSolution6" aria-labelledby="headingSolution6">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb41">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -8785,7 +8785,7 @@ <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="#collapseSolution7" aria-expanded="false" aria-controls="collapseSolution7">
   <h4 class="accordion-header" id="headingSolution7"> Show me the solution </h4>
 </button>
-<div id="collapseSolution7" class="accordion-collapse collapse" aria-labelledby="headingSolution7" data-bs-parent="#accordionSolution7">
+<div id="collapseSolution7" class="accordion-collapse collapse" data-bs-parent="#accordionSolution7" aria-labelledby="headingSolution7">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb45">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -8880,7 +8880,7 @@ <h3 class="callout-title">Combining operators</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution8" aria-expanded="false" aria-controls="collapseSolution8">
   <h4 class="accordion-header" id="headingSolution8"> Show me the solution </h4>
 </button>
-<div id="collapseSolution8" class="accordion-collapse collapse" aria-labelledby="headingSolution8" data-bs-parent="#accordionSolution8">
+<div id="collapseSolution8" class="accordion-collapse collapse" data-bs-parent="#accordionSolution8" aria-labelledby="headingSolution8">
 <div class="accordion-body">
 <p>You need to use the <code>mix</code> operator first to combine the
 channels followed by the <code>collect</code> operator to collect all
@@ -9051,7 +9051,7 @@ <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="#collapseSolution9" aria-expanded="false" aria-controls="collapseSolution9">
   <h4 class="accordion-header" id="headingSolution9"> Show me the solution </h4>
 </button>
-<div id="collapseSolution9" class="accordion-collapse collapse" aria-labelledby="headingSolution9" data-bs-parent="#accordionSolution9">
+<div id="collapseSolution9" class="accordion-collapse collapse" data-bs-parent="#accordionSolution9" aria-labelledby="headingSolution9">
 <div class="accordion-body">
 <p>The <code>INDEX</code> process should be the longest running process.
 dag.png <img src="fig/dag.png" alt="dag" class="figure"> The vertices in the graph
@@ -10105,8 +10105,8 @@ <h3 class="callout-title">Key Points</h3>
   "url": "https://carpentries-incubator.github.io/workflows-nextflow/aio.html",
   "identifier": "https://carpentries-incubator.github.io/workflows-nextflow/aio.html",
   "dateCreated": "2021-02-01",
-  "dateModified": "2024-10-22",
-  "datePublished": "2024-10-22"
+  "dateModified": "2024-10-29",
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/discuss.html b/discuss.html
index f0a82831..244591f6 100644
--- a/discuss.html
+++ b/discuss.html
@@ -442,7 +442,7 @@ <h1>Discussion</h1>
   "identifier": "https://carpentries-incubator.github.io/workflows-nextflow/discuss.html",
   "dateCreated": "2021-02-01",
   "dateModified": "2024-02-15",
-  "datePublished": "2024-10-22"
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/images.html b/images.html
index 5d99595e..cd1e00d7 100644
--- a/images.html
+++ b/images.html
@@ -580,8 +580,8 @@ <h3 id="12-nfcore-figure-2">Figure 2</h3>
   "url": "https://carpentries-incubator.github.io/workflows-nextflow/images.html",
   "identifier": "https://carpentries-incubator.github.io/workflows-nextflow/images.html",
   "dateCreated": "2021-02-01",
-  "dateModified": "2024-10-22",
-  "datePublished": "2024-10-22"
+  "dateModified": "2024-10-29",
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/index.html b/index.html
index fe54f597..5a0c45bc 100644
--- a/index.html
+++ b/index.html
@@ -662,8 +662,8 @@ <h2 id="running-exercises-remotely-in-your-web-browser-through-gitpod-">Running
   "url": "https://carpentries-incubator.github.io/workflows-nextflow/index.html",
   "identifier": "https://carpentries-incubator.github.io/workflows-nextflow/index.html",
   "dateCreated": "2021-02-01",
-  "dateModified": "2024-10-22",
-  "datePublished": "2024-10-22"
+  "dateModified": "2024-10-29",
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/instructor-notes.html b/instructor-notes.html
index 82df1ee8..5caf9b9f 100644
--- a/instructor-notes.html
+++ b/instructor-notes.html
@@ -592,8 +592,8 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
   "url": "https://carpentries-incubator.github.io/workflows-nextflow/instructor-notes.html",
   "identifier": "https://carpentries-incubator.github.io/workflows-nextflow/instructor-notes.html",
   "dateCreated": "2021-02-01",
-  "dateModified": "2024-10-22",
-  "datePublished": "2024-10-22"
+  "dateModified": "2024-10-29",
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/instructor/01-getting-started-with-nextflow.html b/instructor/01-getting-started-with-nextflow.html
index d459ce23..b65f0e6e 100644
--- a/instructor/01-getting-started-with-nextflow.html
+++ b/instructor/01-getting-started-with-nextflow.html
@@ -798,7 +798,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/workflows-nextflow/instructor/01-getting-started-with-nextflow.html",
   "dateCreated": "2021-02-01",
   "dateModified": "2024-06-10",
-  "datePublished": "2024-10-22"
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/instructor/02-workflow_parameters.html b/instructor/02-workflow_parameters.html
index 88060d92..6d988072 100644
--- a/instructor/02-workflow_parameters.html
+++ b/instructor/02-workflow_parameters.html
@@ -805,7 +805,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/workflows-nextflow/instructor/02-workflow_parameters.html",
   "dateCreated": "2021-02-01",
   "dateModified": "2024-08-23",
-  "datePublished": "2024-10-22"
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/instructor/03-channels.html b/instructor/03-channels.html
index fbe4bc43..e1be2e81 100644
--- a/instructor/03-channels.html
+++ b/instructor/03-channels.html
@@ -1203,7 +1203,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/workflows-nextflow/instructor/03-channels.html",
   "dateCreated": "2021-02-01",
   "dateModified": "2024-08-23",
-  "datePublished": "2024-10-22"
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/instructor/04-processes-part1.html b/instructor/04-processes-part1.html
index 806bbf41..b78e0fb9 100644
--- a/instructor/04-processes-part1.html
+++ b/instructor/04-processes-part1.html
@@ -2032,7 +2032,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/workflows-nextflow/instructor/04-processes-part1.html",
   "dateCreated": "2021-02-01",
   "dateModified": "2024-08-23",
-  "datePublished": "2024-10-22"
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/instructor/05-processes-part2.html b/instructor/05-processes-part2.html
index 61a06d29..8977462d 100644
--- a/instructor/05-processes-part2.html
+++ b/instructor/05-processes-part2.html
@@ -1506,7 +1506,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/workflows-nextflow/instructor/05-processes-part2.html",
   "dateCreated": "2021-02-01",
   "dateModified": "2024-06-10",
-  "datePublished": "2024-10-22"
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/instructor/06-workflow.html b/instructor/06-workflow.html
index 03a685cc..2b9f162a 100644
--- a/instructor/06-workflow.html
+++ b/instructor/06-workflow.html
@@ -816,7 +816,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/workflows-nextflow/instructor/06-workflow.html",
   "dateCreated": "2021-02-01",
   "dateModified": "2024-06-10",
-  "datePublished": "2024-10-22"
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/instructor/07-operators.html b/instructor/07-operators.html
index 2f5fdec3..884c445f 100644
--- a/instructor/07-operators.html
+++ b/instructor/07-operators.html
@@ -1383,7 +1383,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/workflows-nextflow/instructor/07-operators.html",
   "dateCreated": "2021-02-01",
   "dateModified": "2024-04-23",
-  "datePublished": "2024-10-22"
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/instructor/08-reporting.html b/instructor/08-reporting.html
index 8fde0da8..11399ce5 100644
--- a/instructor/08-reporting.html
+++ b/instructor/08-reporting.html
@@ -466,7 +466,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>The output will look similar to this:</p>
 <div class="codewrapper">
@@ -641,7 +641,7 @@ <h3 class="callout-title">View run log</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>Example solution using run name <code>elegant_descartes</code>.</p>
 <div class="codewrapper sourceCode" id="cb13">
@@ -670,7 +670,7 @@ <h3 class="callout-title">Filter pipeline run log</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb14">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -754,7 +754,7 @@ <h3 class="callout-title">Generate an HTML run report</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb19">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -838,7 +838,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/workflows-nextflow/instructor/08-reporting.html",
   "dateCreated": "2021-02-01",
   "dateModified": "2024-04-23",
-  "datePublished": "2024-10-22"
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/instructor/09-configuration.html b/instructor/09-configuration.html
index dc0e99c8..ec42801b 100644
--- a/instructor/09-configuration.html
+++ b/instructor/09-configuration.html
@@ -1412,7 +1412,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/workflows-nextflow/instructor/09-configuration.html",
   "dateCreated": "2021-02-01",
   "dateModified": "2024-06-10",
-  "datePublished": "2024-10-22"
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/instructor/10-workflow_checkpoint_caching.html b/instructor/10-workflow_checkpoint_caching.html
index 92d068c2..80d2aaab 100644
--- a/instructor/10-workflow_checkpoint_caching.html
+++ b/instructor/10-workflow_checkpoint_caching.html
@@ -470,7 +470,7 @@ <h3 class="callout-title">Resume a pipeline</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" 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">
 <div class="codewrapper sourceCode" id="cb3">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -570,7 +570,7 @@ <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>The output will look similar to this:</p>
 <div class="codewrapper">
@@ -782,7 +782,7 @@ <h3 class="callout-title">Remove a Nextflow run.</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <p>An example nextflow clean command with <code>dry-run</code> .</p>
 <div class="codewrapper sourceCode" id="cb14">
@@ -878,7 +878,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/workflows-nextflow/instructor/10-workflow_checkpoint_caching.html",
   "dateCreated": "2021-02-01",
   "dateModified": "2024-08-21",
-  "datePublished": "2024-10-22"
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/instructor/11-Simple_Rna-Seq_pipeline.html b/instructor/11-Simple_Rna-Seq_pipeline.html
index df0cee4b..2286bb38 100644
--- a/instructor/11-Simple_Rna-Seq_pipeline.html
+++ b/instructor/11-Simple_Rna-Seq_pipeline.html
@@ -548,7 +548,7 @@ <h3 class="callout-title">Add a parameter</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">
 <div class="codewrapper sourceCode" id="cb10">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -597,7 +597,7 @@ <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" 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>Below is an example log.info command printing all the pipeline
 parameters.</p>
@@ -781,7 +781,7 @@ <h3 class="callout-title">View the contents of the index_ch</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb22">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -928,7 +928,7 @@ <h3 class="callout-title">Read in all read pairs</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb32">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1071,7 +1071,7 @@ <h3 class="callout-title">Add a tag directive</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
   <h4 class="accordion-header" id="headingSolution5"> Show me the solution </h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb40">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1113,7 +1113,7 @@ <h3 class="callout-title">Challenge</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution6" aria-expanded="false" aria-controls="collapseSolution6">
   <h4 class="accordion-header" id="headingSolution6"> Show me the solution </h4>
 </button>
-<div id="collapseSolution6" class="accordion-collapse collapse" aria-labelledby="headingSolution6" data-bs-parent="#accordionSolution6">
+<div id="collapseSolution6" class="accordion-collapse collapse" data-bs-parent="#accordionSolution6" aria-labelledby="headingSolution6">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb41">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1210,7 +1210,7 @@ <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="#collapseSolution7" aria-expanded="false" aria-controls="collapseSolution7">
   <h4 class="accordion-header" id="headingSolution7"> Show me the solution </h4>
 </button>
-<div id="collapseSolution7" class="accordion-collapse collapse" aria-labelledby="headingSolution7" data-bs-parent="#accordionSolution7">
+<div id="collapseSolution7" class="accordion-collapse collapse" data-bs-parent="#accordionSolution7" aria-labelledby="headingSolution7">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb45">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1294,7 +1294,7 @@ <h3 class="callout-title">Combining operators</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution8" aria-expanded="false" aria-controls="collapseSolution8">
   <h4 class="accordion-header" id="headingSolution8"> Show me the solution </h4>
 </button>
-<div id="collapseSolution8" class="accordion-collapse collapse" aria-labelledby="headingSolution8" data-bs-parent="#accordionSolution8">
+<div id="collapseSolution8" class="accordion-collapse collapse" data-bs-parent="#accordionSolution8" aria-labelledby="headingSolution8">
 <div class="accordion-body">
 <p>You need to use the <code>mix</code> operator first to combine the
 channels followed by the <code>collect</code> operator to collect all
@@ -1454,7 +1454,7 @@ <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="#collapseSolution9" aria-expanded="false" aria-controls="collapseSolution9">
   <h4 class="accordion-header" id="headingSolution9"> Show me the solution </h4>
 </button>
-<div id="collapseSolution9" class="accordion-collapse collapse" aria-labelledby="headingSolution9" data-bs-parent="#accordionSolution9">
+<div id="collapseSolution9" class="accordion-collapse collapse" data-bs-parent="#accordionSolution9" aria-labelledby="headingSolution9">
 <div class="accordion-body">
 <p>The <code>INDEX</code> process should be the longest running process.
 dag.png <img src="../fig/dag.png" alt="dag" class="figure"> The vertices in the graph
@@ -1566,7 +1566,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/workflows-nextflow/instructor/11-Simple_Rna-Seq_pipeline.html",
   "dateCreated": "2021-02-01",
   "dateModified": "2024-09-27",
-  "datePublished": "2024-10-22"
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/instructor/12-nfcore.html b/instructor/12-nfcore.html
index 57e68139..3ce62ac3 100644
--- a/instructor/12-nfcore.html
+++ b/instructor/12-nfcore.html
@@ -1348,7 +1348,7 @@ <h3 class="callout-title">Key Points</h3>
   "identifier": "https://carpentries-incubator.github.io/workflows-nextflow/instructor/12-nfcore.html",
   "dateCreated": "2021-02-01",
   "dateModified": "2024-07-22",
-  "datePublished": "2024-10-22"
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/instructor/404.html b/instructor/404.html
index cfbff38a..dc098682 100644
--- a/instructor/404.html
+++ b/instructor/404.html
@@ -440,8 +440,8 @@ <h1>Page not found</h1>
   "url": "https://carpentries-incubator.github.io/workflows-nextflow/instructor/404.html",
   "identifier": "https://carpentries-incubator.github.io/workflows-nextflow/instructor/404.html",
   "dateCreated": "2021-02-01",
-  "dateModified": "2024-10-22",
-  "datePublished": "2024-10-22"
+  "dateModified": "2024-10-29",
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/instructor/CODE_OF_CONDUCT.html b/instructor/CODE_OF_CONDUCT.html
index db80ad9c..1c273314 100644
--- a/instructor/CODE_OF_CONDUCT.html
+++ b/instructor/CODE_OF_CONDUCT.html
@@ -451,7 +451,7 @@ <h1>Contributor Code of Conduct</h1>
   "identifier": "https://carpentries-incubator.github.io/workflows-nextflow/instructor/CODE_OF_CONDUCT.html",
   "dateCreated": "2021-02-01",
   "dateModified": "2023-12-08",
-  "datePublished": "2024-10-22"
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/instructor/LICENSE.html b/instructor/LICENSE.html
index 255e598d..882aad68 100644
--- a/instructor/LICENSE.html
+++ b/instructor/LICENSE.html
@@ -499,7 +499,7 @@ <h1>Licenses</h1>
   "identifier": "https://carpentries-incubator.github.io/workflows-nextflow/instructor/LICENSE.html",
   "dateCreated": "2021-02-01",
   "dateModified": "2023-12-08",
-  "datePublished": "2024-10-22"
+  "datePublished": "2024-10-29"
 }
 
   </script><script>
diff --git a/instructor/aio.html b/instructor/aio.html
index 3e3feec8..aed4fb5e 100644
--- a/instructor/aio.html
+++ b/instructor/aio.html
@@ -6203,7 +6203,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>The output will look similar to this:</p>
 <div class="codewrapper">
@@ -6386,7 +6386,7 @@ <h3 class="callout-title">View run log</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>Example solution using run name <code>elegant_descartes</code>.</p>
 <div class="codewrapper sourceCode" id="cb13">
@@ -6415,7 +6415,7 @@ <h3 class="callout-title">Filter pipeline run log</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb14">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -6501,7 +6501,7 @@ <h3 class="callout-title">Generate an HTML run report</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb19">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -7639,7 +7639,7 @@ <h3 class="callout-title">Resume a pipeline</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" 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">
 <div class="codewrapper sourceCode" id="cb3">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -7745,7 +7745,7 @@ <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>The output will look similar to this:</p>
 <div class="codewrapper">
@@ -7964,7 +7964,7 @@ <h3 class="callout-title">Remove a Nextflow run.</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <p>An example nextflow clean command with <code>dry-run</code> .</p>
 <div class="codewrapper sourceCode" id="cb14">
@@ -8172,7 +8172,7 @@ <h3 class="callout-title">Add a parameter</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">
 <div class="codewrapper sourceCode" id="cb10">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -8221,7 +8221,7 @@ <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" 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>Below is an example log.info command printing all the pipeline
 parameters.</p>
@@ -8416,7 +8416,7 @@ <h3 class="callout-title">View the contents of the index_ch</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb22">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -8570,7 +8570,7 @@ <h3 class="callout-title">Read in all read pairs</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution4" aria-expanded="false" aria-controls="collapseSolution4">
   <h4 class="accordion-header" id="headingSolution4"> Show me the solution </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb32">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -8720,7 +8720,7 @@ <h3 class="callout-title">Add a tag directive</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution5" aria-expanded="false" aria-controls="collapseSolution5">
   <h4 class="accordion-header" id="headingSolution5"> Show me the solution </h4>
 </button>
-<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb40">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -8764,7 +8764,7 @@ <h3 class="callout-title">Challenge</h3>
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@@ -8961,7 +8961,7 @@ <h3 class="callout-title">Combining operators</h3>
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 <p>You need to use the <code>mix</code> operator first to combine the
 channels followed by the <code>collect</code> operator to collect all
@@ -9132,7 +9132,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
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 <p>The <code>INDEX</code> process should be the longest running process.
 dag.png <img src="../fig/dag.png" alt="dag" class="figure"> The vertices in the graph
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