From c5c25046c0b0f7c6a95a220950f0ebba2d24d2ca Mon Sep 17 00:00:00 2001
From: GitHub Actions <actions@github.com>
Date: Tue, 24 Sep 2024 01:00:45 +0000
Subject: [PATCH] site deploy

Auto-generated via {sandpaper}
Source  : a87a2ae50f53aa4b50f93bf1a3d47814f9ead1c4
Branch  : md-outputs
Author  : GitHub Actions <actions@github.com>
Time    : 2024-08-26 13:50:11 +0000
Message : markdown source builds

Auto-generated via {sandpaper}
Source  : 6ce95f99b52ab586f14641afa6b68c6cc42e7e6e
Branch  : main
Author  : Graeme Grimes <graeme.grimes@ed.ac.uk>
Time    : 2024-08-26 13:49:09 +0000
Message : Merge pull request #159 from mahesh-panchal/update_gitpod

Update Carpentries Gitpod environment
---
 01-getting-started-with-nextflow.html         |  2 +-
 02-workflow_parameters.html                   |  8 +--
 03-channels.html                              |  2 +-
 04-processes-part1.html                       |  2 +-
 05-processes-part2.html                       | 10 ++--
 06-workflow.html                              |  2 +-
 07-operators.html                             | 10 ++--
 08-reporting.html                             |  2 +-
 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                                      | 50 +++++++++----------
 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        |  8 +--
 instructor/03-channels.html                   |  2 +-
 instructor/04-processes-part1.html            |  2 +-
 instructor/05-processes-part2.html            | 10 ++--
 instructor/06-workflow.html                   |  2 +-
 instructor/07-operators.html                  | 10 ++--
 instructor/08-reporting.html                  |  2 +-
 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                           | 50 +++++++++----------
 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                                   |  4 +-
 profiles.html                                 |  4 +-
 reference.html                                |  2 +-
 49 files changed, 156 insertions(+), 156 deletions(-)

diff --git a/01-getting-started-with-nextflow.html b/01-getting-started-with-nextflow.html
index 70fe9428..85a77426 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": "2024-09-17"
+  "datePublished": "2024-09-24"
 }
 
   </script><script>
diff --git a/02-workflow_parameters.html b/02-workflow_parameters.html
index 6b624bd0..f8368b01 100644
--- a/02-workflow_parameters.html
+++ b/02-workflow_parameters.html
@@ -498,7 +498,7 @@ <h3 class="callout-title">Change a pipeline’s input using 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="cb5">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -606,7 +606,7 @@ <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">
 <div class="codewrapper sourceCode" id="cb12">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -701,7 +701,7 @@ <h3 class="callout-title">Create and use a Parameter file.</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="cb19">
 <h3 class="code-label">JSON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -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": "2024-09-17"
+  "datePublished": "2024-09-24"
 }
 
   </script><script>
diff --git a/03-channels.html b/03-channels.html
index c099ad35..b529ab0d 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": "2024-09-17"
+  "datePublished": "2024-09-24"
 }
 
   </script><script>
diff --git a/04-processes-part1.html b/04-processes-part1.html
index 3faa44c7..cbe25779 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": "2024-09-17"
+  "datePublished": "2024-09-24"
 }
 
   </script><script>
diff --git a/05-processes-part2.html b/05-processes-part2.html
index 90e9bcd4..92a5c88f 100644
--- a/05-processes-part2.html
+++ b/05-processes-part2.html
@@ -675,7 +675,7 @@ <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"><
 <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>
@@ -851,7 +851,7 @@ <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"><
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb19">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1076,7 +1076,7 @@ <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"><
 <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"> 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="cb26">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1364,7 +1364,7 @@ <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"><
 <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="cb41">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -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": "2024-09-17"
+  "datePublished": "2024-09-24"
 }
 
   </script><script>
diff --git a/06-workflow.html b/06-workflow.html
index bdaba057..ffc10eab 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": "2024-09-17"
+  "datePublished": "2024-09-24"
 }
 
   </script><script>
diff --git a/07-operators.html b/07-operators.html
index 2b6ddb0a..63148d99 100644
--- a/07-operators.html
+++ b/07-operators.html
@@ -723,7 +723,7 @@ <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"><
 <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="cb20">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -860,7 +860,7 @@ <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"><
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb29">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1012,7 +1012,7 @@ <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"><
 <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="cb42">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1261,7 +1261,7 @@ <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"><
 <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="cb59">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -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": "2024-09-17"
+  "datePublished": "2024-09-24"
 }
 
   </script><script>
diff --git a/08-reporting.html b/08-reporting.html
index c9531817..be283d1d 100644
--- a/08-reporting.html
+++ b/08-reporting.html
@@ -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": "2024-09-17"
+  "datePublished": "2024-09-24"
 }
 
   </script><script>
diff --git a/09-configuration.html b/09-configuration.html
index 9f49eb7d..85d8c611 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": "2024-09-17"
+  "datePublished": "2024-09-24"
 }
 
   </script><script>
diff --git a/10-workflow_checkpoint_caching.html b/10-workflow_checkpoint_caching.html
index 52d482b0..903e2788 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" 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="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" 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 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" 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>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": "2024-09-17"
+  "datePublished": "2024-09-24"
 }
 
   </script><script>
diff --git a/11-Simple_Rna-Seq_pipeline.html b/11-Simple_Rna-Seq_pipeline.html
index 64c7c374..1f4cb160 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">Combing 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": "2024-06-10",
-  "datePublished": "2024-09-17"
+  "datePublished": "2024-09-24"
 }
 
   </script><script>
diff --git a/12-nfcore.html b/12-nfcore.html
index f5c7bc24..dcdfbbdf 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": "2024-09-17"
+  "datePublished": "2024-09-24"
 }
 
   </script><script>
diff --git a/404.html b/404.html
index 44f6a301..8540aede 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": "2024-09-17",
-  "datePublished": "2024-09-17"
+  "dateModified": "2024-09-24",
+  "datePublished": "2024-09-24"
 }
 
   </script><script>
diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html
index f7c35065..b0c98491 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": "2024-09-17"
+  "datePublished": "2024-09-24"
 }
 
   </script><script>
diff --git a/LICENSE.html b/LICENSE.html
index 7155844a..08a74e82 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": "2024-09-17"
+  "datePublished": "2024-09-24"
 }
 
   </script><script>
diff --git a/aio.html b/aio.html
index a76aef38..6cf0efa2 100644
--- a/aio.html
+++ b/aio.html
@@ -916,7 +916,7 @@ <h3 class="callout-title">Change a pipeline’s input using 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="cb5">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1026,7 +1026,7 @@ <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">
 <div class="codewrapper sourceCode" id="cb12">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1125,7 +1125,7 @@ <h3 class="callout-title">Create and use a Parameter file.</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="cb19">
 <h3 class="code-label">JSON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -3909,7 +3909,7 @@ <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"><
 <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>
@@ -4086,7 +4086,7 @@ <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"><
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb19">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -4317,7 +4317,7 @@ <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"><
 <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"> 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="cb26">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -4610,7 +4610,7 @@ <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"><
 <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="cb41">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -5434,7 +5434,7 @@ <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"><
 <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="cb20">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -5574,7 +5574,7 @@ <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"><
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb29">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -5729,7 +5729,7 @@ <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"><
 <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="cb42">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -5991,7 +5991,7 @@ <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"><
 <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="cb59">
 <h3 class="code-label">GROOVY<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" 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="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" 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 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" 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>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">
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 <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">Combing 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": "2024-06-10",
-  "datePublished": "2024-09-17"
+  "datePublished": "2024-09-24"
 }
 
   </script><script>
diff --git a/instructor/12-nfcore.html b/instructor/12-nfcore.html
index badca0d1..0dcf3a26 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": "2024-09-17"
+  "datePublished": "2024-09-24"
 }
 
   </script><script>
diff --git a/instructor/404.html b/instructor/404.html
index 6eb967bd..8bea1a6f 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": "2024-09-17",
-  "datePublished": "2024-09-17"
+  "dateModified": "2024-09-24",
+  "datePublished": "2024-09-24"
 }
 
   </script><script>
diff --git a/instructor/CODE_OF_CONDUCT.html b/instructor/CODE_OF_CONDUCT.html
index a8a24994..977479f7 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": "2024-09-17"
+  "datePublished": "2024-09-24"
 }
 
   </script><script>
diff --git a/instructor/LICENSE.html b/instructor/LICENSE.html
index b3d4c796..000e44d6 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": "2024-09-17"
+  "datePublished": "2024-09-24"
 }
 
   </script><script>
diff --git a/instructor/aio.html b/instructor/aio.html
index 825de003..454e12ef 100644
--- a/instructor/aio.html
+++ b/instructor/aio.html
@@ -942,7 +942,7 @@ <h3 class="callout-title">Change a pipeline’s input using 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="cb5">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1052,7 +1052,7 @@ <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">
 <div class="codewrapper sourceCode" id="cb12">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1151,7 +1151,7 @@ <h3 class="callout-title">Create and use a Parameter file.</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="cb19">
 <h3 class="code-label">JSON<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -3970,7 +3970,7 @@ <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"><
 <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>
@@ -4147,7 +4147,7 @@ <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"><
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb19">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -4378,7 +4378,7 @@ <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"><
 <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"> 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="cb26">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -4671,7 +4671,7 @@ <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"><
 <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="cb41">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -5497,7 +5497,7 @@ <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"><
 <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="cb20">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -5637,7 +5637,7 @@ <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"><
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb29">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -5792,7 +5792,7 @@ <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"><
 <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="cb42">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -6054,7 +6054,7 @@ <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"><
 <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="cb59">
 <h3 class="code-label">GROOVY<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" 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="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" 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 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" 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>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">
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-<div id="collapseSolution7" class="accordion-collapse collapse" aria-labelledby="headingSolution7" data-bs-parent="#accordionSolution7">
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-<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
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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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