From 1f9c3bb025fd0dbecfe2280aecda90059d7cd6bb Mon Sep 17 00:00:00 2001
From: GitHub Actions <actions@github.com>
Date: Tue, 10 Dec 2024 00:31:02 +0000
Subject: [PATCH] site deploy

Auto-generated via `{sandpaper}`
Source  : 2946f35efeee737d960ebaaeb052038857b4cbe8
Branch  : md-outputs
Author  : GitHub Actions <actions@github.com>
Time    : 2024-12-10 00:30:47 +0000
Message : markdown source builds

Auto-generated via `{sandpaper}`
Source  : 0f4fef36d62e3c04d31602aee73b306e2e3764bc
Branch  : main
Author  : Alexis Lucattini <alexis.lucattini@umccr.org>
Time    : 2024-05-09 03:25:09 +0000
Message : Merge pull request #32 from umccr/enhancement/update-challenge-format

Update challenge format
---
 01-introduction.html                 |  6 +--
 02-shell_to_cwl.html                 | 24 +++++-----
 03-dependency_graphs.html            | 18 ++++----
 04-reusing_tools.html                | 16 +++----
 404.html                             |  4 +-
 CODE_OF_CONDUCT.html                 |  6 +--
 LICENSE.html                         |  6 +--
 addendum-01-debug.html               | 16 +++----
 aio.html                             | 66 +++++++++++++--------------
 images.html                          |  4 +-
 index.html                           |  4 +-
 instructor-notes.html                |  4 +-
 instructor/01-introduction.html      |  6 +--
 instructor/02-shell_to_cwl.html      | 26 +++++------
 instructor/03-dependency_graphs.html | 18 ++++----
 instructor/04-reusing_tools.html     | 16 +++----
 instructor/404.html                  |  4 +-
 instructor/CODE_OF_CONDUCT.html      |  6 +--
 instructor/LICENSE.html              |  6 +--
 instructor/addendum-01-debug.html    | 16 +++----
 instructor/aio.html                  | 68 ++++++++++++++--------------
 instructor/images.html               |  4 +-
 instructor/index.html                |  4 +-
 instructor/instructor-notes.html     |  4 +-
 instructor/key-points.html           |  4 +-
 instructor/more_info.html            |  6 +--
 instructor/profiles.html             |  4 +-
 instructor/reference.html            |  6 +--
 key-points.html                      |  4 +-
 md5sum.txt                           | 36 +++++++--------
 more_info.html                       |  6 +--
 pkgdown.yml                          |  2 +-
 profiles.html                        |  4 +-
 reference.html                       |  6 +--
 34 files changed, 215 insertions(+), 215 deletions(-)

diff --git a/01-introduction.html b/01-introduction.html
index 17b42c9..6cb5b60 100644
--- a/01-introduction.html
+++ b/01-introduction.html
@@ -331,7 +331,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Introduction</h1>
-        <p>Last updated on 2024-12-03 |
+        <p>Last updated on 2024-12-10 |
 
         <a href="https://github.com/__USERNAME__/__PROJECT__/edit/main/episodes/01-introduction.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 
@@ -639,8 +639,8 @@ <h3 class="callout-title">Key Points</h3>
   "url": "https://__USERNAME__.github.io/__PROJECT__/01-introduction.html",
   "identifier": "https://__USERNAME__.github.io/__PROJECT__/01-introduction.html",
   "dateCreated": "2024-04-29",
-  "dateModified": "2024-12-03",
-  "datePublished": "2024-12-03"
+  "dateModified": "2024-12-10",
+  "datePublished": "2024-12-10"
 }
 
   </script><script>
diff --git a/02-shell_to_cwl.html b/02-shell_to_cwl.html
index bfb9131..dfb9222 100644
--- a/02-shell_to_cwl.html
+++ b/02-shell_to_cwl.html
@@ -327,7 +327,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>CWL and Shell Tools</h1>
-        <p>Last updated on 2024-12-03 |
+        <p>Last updated on 2024-12-10 |
 
         <a href="https://github.com/__USERNAME__/__PROJECT__/edit/main/episodes/02-shell_to_cwl.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 
@@ -444,7 +444,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler1" aria-expanded="false" aria-controls="collapseSpoiler1">
   <h3 class="accordion-header" id="headingSpoiler1">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> Tool Output </h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
 <div class="accordion-body">
 <pre class="text"><code>INFO Resolved 'echo.cwl' to 'file:///.../echo.cwl'
 INFO [job echo.cwl] /private/tmp/docker_tmprm65mucw$ echo \
@@ -559,7 +559,7 @@ <h3 class="callout-title">Changing the output string 🌶</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>To change the text on the command line, you only have to change the
 text in the <code>hello_world.yml</code> file.</p>
@@ -590,7 +590,7 @@ <h3 class="callout-title">Updating the arguments 🌶🌶</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">
 <div class="codewrapper sourceCode" id="cb10">
 <h3 class="code-label">YAML<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -624,7 +624,7 @@ <h3 class="callout-title">Redirecting cwltool stdout and stderr 🌶🌶</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Hint: Redirecting CLI stdout and stderr </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>Use the redirectors <code>1&gt;</code> and <code>2&gt;</code> to
 redirect stdout and stderr to different files respectively</p>
@@ -637,7 +637,7 @@ <h4 class="accordion-header" id="headingHint1"> Hint: Redirecting CLI stdout and
 <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="cb11">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -672,7 +672,7 @@ <h3 class="callout-title">Specifying the stdout of the tool as a CWL output 🌶
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Hint - stdout output binding </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
 <div class="accordion-body">
 <p>Copy the ‘outputBinding’ from the tutorial ‘verbatim’.</p>
 <p>Your output key should look like this</p>
@@ -696,7 +696,7 @@ <h3 class="code-label">YAML<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="#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="cb13">
 <h3 class="code-label">YAML<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -940,7 +940,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler2" aria-expanded="false" aria-controls="collapseSpoiler2">
   <h3 class="accordion-header" id="headingSpoiler2">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> Console Outputs </h3>
 </button>
-<div id="collapseSpoiler2" class="accordion-collapse collapse" aria-labelledby="headingSpoiler2" data-bs-parent="#accordionSpoiler2">
+<div id="collapseSpoiler2" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler2" aria-labelledby="headingSpoiler2">
 <div class="accordion-body">
 <pre><code>...
 Analysis complete for GSM461177_2_subsampled.fastqsanger
@@ -1000,7 +1000,7 @@ <h3 class="callout-title">Directly embed a Commandlinetool into a file 🌶🌶<
 <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">
 <p>The <code>run</code> field in the step can be replaced with the
 <code>CommandLineTool</code> definition.</p>
@@ -1123,8 +1123,8 @@ <h3 class="callout-title">Key Points</h3>
   "url": "https://__USERNAME__.github.io/__PROJECT__/02-shell_to_cwl.html",
   "identifier": "https://__USERNAME__.github.io/__PROJECT__/02-shell_to_cwl.html",
   "dateCreated": "2024-04-29",
-  "dateModified": "2024-12-03",
-  "datePublished": "2024-12-03"
+  "dateModified": "2024-12-10",
+  "datePublished": "2024-12-10"
 }
 
   </script><script>
diff --git a/03-dependency_graphs.html b/03-dependency_graphs.html
index 220aeb3..5c98c2a 100644
--- a/03-dependency_graphs.html
+++ b/03-dependency_graphs.html
@@ -328,7 +328,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Developing Multi-Step Workflows</h1>
-        <p>Last updated on 2024-12-03 |
+        <p>Last updated on 2024-12-10 |
 
         <a href="https://github.com/__USERNAME__/__PROJECT__/edit/main/episodes/03-dependency_graphs.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 
@@ -404,7 +404,7 @@ <h3 class="callout-title">Naming steps</h3>
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler1" aria-expanded="false" aria-controls="collapseSpoiler1">
   <h3 class="accordion-header" id="headingSpoiler1">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> rna_seq_workflow_2.cwl (Click to expand) </h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb1">
 <h3 class="code-label">YAML<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -549,7 +549,7 @@ <h3 class="callout-title">Is this a valid workflow? 🌶</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="cb2">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -583,7 +583,7 @@ <h3 class="callout-title">Should we be concerned about this warning 🌶🌶🌶
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <p>In this case, the outputs of the mapping step may instead either be
 just one file, OR an array of files.</p>
@@ -602,7 +602,7 @@ <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler2" aria-expanded="false" aria-controls="collapseSpoiler2">
   <h3 class="accordion-header" id="headingSpoiler2">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> workflow_input_2.yml (Click to expand) </h3>
 </button>
-<div id="collapseSpoiler2" class="accordion-collapse collapse" aria-labelledby="headingSpoiler2" data-bs-parent="#accordionSpoiler2">
+<div id="collapseSpoiler2" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler2" aria-labelledby="headingSpoiler2">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb4">
 <h3 class="code-label">YAML<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -651,7 +651,7 @@ <h3 class="callout-title">Challenge: Draw the workflow 🌶</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>To find out how the inputs and the steps are connected to each other,
 look at the <code>in</code> field of the different steps.</p>
@@ -727,7 +727,7 @@ <h3 class="callout-title">Push your workflow to GitHub 🌶</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"> Git add / commit / push </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
 <div class="accordion-body">
 <p>Your solution might look like this</p>
 <div class="codewrapper sourceCode" id="cb6">
@@ -883,8 +883,8 @@ <h3 class="callout-title">Key Points</h3>
   "url": "https://__USERNAME__.github.io/__PROJECT__/03-dependency_graphs.html",
   "identifier": "https://__USERNAME__.github.io/__PROJECT__/03-dependency_graphs.html",
   "dateCreated": "2024-04-29",
-  "dateModified": "2024-12-03",
-  "datePublished": "2024-12-03"
+  "dateModified": "2024-12-10",
+  "datePublished": "2024-12-10"
 }
 
   </script><script>
diff --git a/04-reusing_tools.html b/04-reusing_tools.html
index 0cfc2bf..0213ef1 100644
--- a/04-reusing_tools.html
+++ b/04-reusing_tools.html
@@ -327,7 +327,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Resources for Reusing Tools and Scripts</h1>
-        <p>Last updated on 2024-12-03 |
+        <p>Last updated on 2024-12-10 |
 
         <a href="https://github.com/__USERNAME__/__PROJECT__/edit/main/episodes/04-reusing_tools.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 
@@ -391,7 +391,7 @@ <h3 class="callout-title">Find the featureCounts tool in the bio-cwl-tools libra
 <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 <code>featureCounts</code> CWL document can be found in the <a href="https://github.com/common-workflow-library/bio-cwl-tools/blob/release/subread/featureCounts.cwl" class="external-link">GitHub
 repo</a>.</p>
@@ -437,7 +437,7 @@ <h3 class="callout-title">Add the featureCounts tool to the workflow 🌶🌶</h
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Hint: Feature Counts Workflow Step </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>Use the <code>run</code> field to add the <code>featureCounts</code>
 tool as a step in the workflow.</p>
@@ -450,7 +450,7 @@ <h4 class="accordion-header" id="headingHint1"> Hint: Feature Counts Workflow St
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Hint: Upgrade RAM </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
 <div class="accordion-body">
 <p>Use a <code>requirements</code> entry with
 <code>ResourceRequirement</code> to allocate a <code>ramMin</code> of
@@ -464,7 +464,7 @@ <h4 class="accordion-header" id="headingHint2"> Hint: Upgrade RAM </h4>
 <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"> Solution: workflow_3.yml (Click to expand) </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="cb1">
 <h3 class="code-label">YAML<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -560,7 +560,7 @@ <h3 class="code-label">YAML<i aria-hidden="true" data-feather="chevron-left"></i
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler1" aria-expanded="false" aria-controls="collapseSpoiler1">
   <h3 class="accordion-header" id="headingSpoiler1">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> workflow_input_3.yml (Click to expand) </h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb2">
 <h3 class="code-label">YAML<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -678,8 +678,8 @@ <h3 class="callout-title">Key Points</h3>
   "url": "https://__USERNAME__.github.io/__PROJECT__/04-reusing_tools.html",
   "identifier": "https://__USERNAME__.github.io/__PROJECT__/04-reusing_tools.html",
   "dateCreated": "2024-04-29",
-  "dateModified": "2024-12-03",
-  "datePublished": "2024-12-03"
+  "dateModified": "2024-12-10",
+  "datePublished": "2024-12-10"
 }
 
   </script><script>
diff --git a/404.html b/404.html
index ce07c87..86324d2 100644
--- a/404.html
+++ b/404.html
@@ -375,8 +375,8 @@ <h1>Page not found</h1>
   "url": "https://__USERNAME__.github.io/__PROJECT__/404.html",
   "identifier": "https://__USERNAME__.github.io/__PROJECT__/404.html",
   "dateCreated": "2024-04-29",
-  "dateModified": "2024-12-03",
-  "datePublished": "2024-12-03"
+  "dateModified": "2024-12-10",
+  "datePublished": "2024-12-10"
 }
 
   </script><script>
diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html
index 55d11da..24665f2 100644
--- a/CODE_OF_CONDUCT.html
+++ b/CODE_OF_CONDUCT.html
@@ -314,7 +314,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Contributor Code of Conduct</h1>
-        <p>Last updated on 2024-12-03 |
+        <p>Last updated on 2024-12-10 |
 
         <a href="https://github.com/__USERNAME__/__PROJECT__/edit/main/CODE_OF_CONDUCT.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 
@@ -407,8 +407,8 @@ <h1>Contributor Code of Conduct</h1>
   "url": "https://__USERNAME__.github.io/__PROJECT__/CODE_OF_CONDUCT.html",
   "identifier": "https://__USERNAME__.github.io/__PROJECT__/CODE_OF_CONDUCT.html",
   "dateCreated": "2024-04-29",
-  "dateModified": "2024-12-03",
-  "datePublished": "2024-12-03"
+  "dateModified": "2024-12-10",
+  "datePublished": "2024-12-10"
 }
 
   </script><script>
diff --git a/LICENSE.html b/LICENSE.html
index 9beab18..3e93d8f 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -314,7 +314,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Licenses</h1>
-        <p>Last updated on 2024-12-03 |
+        <p>Last updated on 2024-12-10 |
 
         <a href="https://github.com/__USERNAME__/__PROJECT__/edit/main/LICENSE.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 
@@ -438,8 +438,8 @@ <h1>Licenses</h1>
   "url": "https://__USERNAME__.github.io/__PROJECT__/LICENSE.html",
   "identifier": "https://__USERNAME__.github.io/__PROJECT__/LICENSE.html",
   "dateCreated": "2024-04-29",
-  "dateModified": "2024-12-03",
-  "datePublished": "2024-12-03"
+  "dateModified": "2024-12-10",
+  "datePublished": "2024-12-10"
 }
 
   </script><script>
diff --git a/addendum-01-debug.html b/addendum-01-debug.html
index 213fd55..9d048a2 100644
--- a/addendum-01-debug.html
+++ b/addendum-01-debug.html
@@ -330,7 +330,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Debugging Workflows</h1>
-        <p>Last updated on 2024-12-03 |
+        <p>Last updated on 2024-12-10 |
 
         <a href="https://github.com/__USERNAME__/__PROJECT__/edit/main/episodes/addendum-01-debug.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 
@@ -419,7 +419,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler1" aria-expanded="false" aria-controls="collapseSpoiler1">
   <h3 class="accordion-header" id="headingSpoiler1">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> Show details </h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
 <div class="accordion-body">
 <pre><code>ERROR Tool definition failed validation:
 while scanning for the next token
@@ -491,7 +491,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler2" aria-expanded="false" aria-controls="collapseSpoiler2">
   <h3 class="accordion-header" id="headingSpoiler2">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> CWLTOOL VALIDATE ERROR MESSAGE </h3>
 </button>
-<div id="collapseSpoiler2" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler2" aria-labelledby="headingSpoiler2">
+<div id="collapseSpoiler2" class="accordion-collapse collapse" aria-labelledby="headingSpoiler2" data-bs-parent="#accordionSpoiler2">
 <div class="accordion-body">
 <pre><code>ERROR Tool definition failed validation:
 rna_seq_workflow_fieldname_fail.cwl:1:1:   Object `rna_seq_workflow_fieldname_fail.cwl` is not valid
@@ -581,7 +581,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler3" aria-expanded="false" aria-controls="collapseSpoiler3">
   <h3 class="accordion-header" id="headingSpoiler3">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> CWLTOOL VALIDATE ERROR MESSAGE </h3>
 </button>
-<div id="collapseSpoiler3" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler3" aria-labelledby="headingSpoiler3">
+<div id="collapseSpoiler3" class="accordion-collapse collapse" aria-labelledby="headingSpoiler3" data-bs-parent="#accordionSpoiler3">
 <div class="accordion-body">
 <pre><code>ERROR Tool definition failed validation:
 rna_seq_workflow_varname_fail.cwl:8:1:  checking field `steps`
@@ -699,7 +699,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler4" aria-expanded="false" aria-controls="collapseSpoiler4">
   <h3 class="accordion-header" id="headingSpoiler4">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> Incompatible type cwltool error message </h3>
 </button>
-<div id="collapseSpoiler4" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler4" aria-labelledby="headingSpoiler4">
+<div id="collapseSpoiler4" class="accordion-collapse collapse" aria-labelledby="headingSpoiler4" data-bs-parent="#accordionSpoiler4">
 <div class="accordion-body">
 <pre><code>rna_seq_workflow_type_fail.cwl:5:3:   Source 'rna_reads_fruitfly' of type "int" is incompatible
 rna_seq_workflow_type_fail.cwl:12:7:   with sink 'reads_file' of type "File"
@@ -799,7 +799,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler5" aria-expanded="false" aria-controls="collapseSpoiler5">
   <h3 class="accordion-header" id="headingSpoiler5">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> Incompatible format error message </h3>
 </button>
-<div id="collapseSpoiler5" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler5" aria-labelledby="headingSpoiler5">
+<div id="collapseSpoiler5" class="accordion-collapse collapse" aria-labelledby="headingSpoiler5" data-bs-parent="#accordionSpoiler5">
 <div class="accordion-body">
 <pre><code>ERROR Exception on step 'mapping_reads'
 ERROR [step mapping_reads] Cannot make job: Expected value of 'ForwardReads' to have format http://edamontology.org/format_1930 but
@@ -877,8 +877,8 @@ <h3 class="accordion-header" id="headingSpoiler5">  <div class="note-square"><i
   "url": "https://__USERNAME__.github.io/__PROJECT__/addendum-01-debug.html",
   "identifier": "https://__USERNAME__.github.io/__PROJECT__/addendum-01-debug.html",
   "dateCreated": "2024-04-29",
-  "dateModified": "2024-12-03",
-  "datePublished": "2024-12-03"
+  "dateModified": "2024-12-10",
+  "datePublished": "2024-12-10"
 }
 
   </script><script>
diff --git a/aio.html b/aio.html
index 64b639f..8ace806 100644
--- a/aio.html
+++ b/aio.html
@@ -366,7 +366,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
         
 <section id="aio-01-introduction"><p>Content from <a href="01-introduction.html">Introduction</a></p>
 <hr>
-<p>Last updated on 2024-12-03 |
+<p>Last updated on 2024-12-10 |
 
         <a href="https://github.com/__USERNAME__/__PROJECT__/edit/main/episodes/01-introduction.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
@@ -653,7 +653,7 @@ <h3 class="callout-title">Key Points</h3>
 </ol>
 </div></section><section id="aio-02-shell_to_cwl"><p>Content from <a href="02-shell_to_cwl.html">CWL and Shell Tools</a></p>
 <hr>
-<p>Last updated on 2024-12-03 |
+<p>Last updated on 2024-12-10 |
 
         <a href="https://github.com/__USERNAME__/__PROJECT__/edit/main/episodes/02-shell_to_cwl.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
@@ -770,7 +770,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler1" aria-expanded="false" aria-controls="collapseSpoiler1">
   <h3 class="accordion-header" id="headingSpoiler1">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> Tool Output </h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
 <div class="accordion-body">
 <pre class="text"><code>INFO Resolved 'echo.cwl' to 'file:///.../echo.cwl'
 INFO [job echo.cwl] /private/tmp/docker_tmprm65mucw$ echo \
@@ -890,7 +890,7 @@ <h3 class="callout-title">Changing the output string 🌶</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>To change the text on the command line, you only have to change the
 text in the <code>hello_world.yml</code> file.</p>
@@ -921,7 +921,7 @@ <h3 class="callout-title">Updating the arguments 🌶🌶</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">
 <div class="codewrapper sourceCode" id="cb10">
 <h3 class="code-label">YAML<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -955,7 +955,7 @@ <h3 class="callout-title">Redirecting cwltool stdout and stderr 🌶🌶</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Hint: Redirecting CLI stdout and stderr </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>Use the redirectors <code>1&gt;</code> and <code>2&gt;</code> to
 redirect stdout and stderr to different files respectively</p>
@@ -968,7 +968,7 @@ <h4 class="accordion-header" id="headingHint1"> Hint: Redirecting CLI stdout and
 <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="cb11">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1003,7 +1003,7 @@ <h3 class="callout-title">Specifying the stdout of the tool as a CWL output 🌶
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Hint - stdout output binding </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
 <div class="accordion-body">
 <p>Copy the ‘outputBinding’ from the tutorial ‘verbatim’.</p>
 <p>Your output key should look like this</p>
@@ -1027,7 +1027,7 @@ <h3 class="code-label">YAML<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="#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="cb13">
 <h3 class="code-label">YAML<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1282,7 +1282,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler2" aria-expanded="false" aria-controls="collapseSpoiler2">
   <h3 class="accordion-header" id="headingSpoiler2">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> Console Outputs </h3>
 </button>
-<div id="collapseSpoiler2" class="accordion-collapse collapse" aria-labelledby="headingSpoiler2" data-bs-parent="#accordionSpoiler2">
+<div id="collapseSpoiler2" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler2" aria-labelledby="headingSpoiler2">
 <div class="accordion-body">
 <pre><code>...
 Analysis complete for GSM461177_2_subsampled.fastqsanger
@@ -1343,7 +1343,7 @@ <h3 class="callout-title">Directly embed a Commandlinetool into a file 🌶🌶<
 <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">
 <p>The <code>run</code> field in the step can be replaced with the
 <code>CommandLineTool</code> definition.</p>
@@ -1412,7 +1412,7 @@ <h3 class="callout-title">Key Points</h3>
 </div>
 </section></section><section id="aio-03-dependency_graphs"><p>Content from <a href="03-dependency_graphs.html">Developing Multi-Step Workflows</a></p>
 <hr>
-<p>Last updated on 2024-12-03 |
+<p>Last updated on 2024-12-10 |
 
         <a href="https://github.com/__USERNAME__/__PROJECT__/edit/main/episodes/03-dependency_graphs.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
@@ -1488,7 +1488,7 @@ <h3 class="callout-title">Naming steps</h3>
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler1" aria-expanded="false" aria-controls="collapseSpoiler1">
   <h3 class="accordion-header" id="headingSpoiler1">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> rna_seq_workflow_2.cwl (Click to expand) </h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb1">
 <h3 class="code-label">YAML<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1635,7 +1635,7 @@ <h3 class="callout-title">Is this a valid workflow? 🌶</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="cb2">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1669,7 +1669,7 @@ <h3 class="callout-title">Should we be concerned about this warning 🌶🌶🌶
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <p>In this case, the outputs of the mapping step may instead either be
 just one file, OR an array of files.</p>
@@ -1690,7 +1690,7 @@ <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler2" aria-expanded="false" aria-controls="collapseSpoiler2">
   <h3 class="accordion-header" id="headingSpoiler2">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> workflow_input_2.yml (Click to expand) </h3>
 </button>
-<div id="collapseSpoiler2" class="accordion-collapse collapse" aria-labelledby="headingSpoiler2" data-bs-parent="#accordionSpoiler2">
+<div id="collapseSpoiler2" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler2" aria-labelledby="headingSpoiler2">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb4">
 <h3 class="code-label">YAML<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1740,7 +1740,7 @@ <h3 class="callout-title">Challenge: Draw the workflow 🌶</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>To find out how the inputs and the steps are connected to each other,
 look at the <code>in</code> field of the different steps.</p>
@@ -1822,7 +1822,7 @@ <h3 class="callout-title">Push your workflow to GitHub 🌶</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"> Git add / commit / push </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
 <div class="accordion-body">
 <p>Your solution might look like this</p>
 <div class="codewrapper sourceCode" id="cb6">
@@ -1927,7 +1927,7 @@ <h3 class="callout-title">Key Points</h3>
 </div>
 </section></section><section id="aio-04-reusing_tools"><p>Content from <a href="04-reusing_tools.html">Resources for Reusing Tools and Scripts</a></p>
 <hr>
-<p>Last updated on 2024-12-03 |
+<p>Last updated on 2024-12-10 |
 
         <a href="https://github.com/__USERNAME__/__PROJECT__/edit/main/episodes/04-reusing_tools.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
@@ -1993,7 +1993,7 @@ <h3 class="callout-title">Find the featureCounts tool in the bio-cwl-tools libra
 <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 <code>featureCounts</code> CWL document can be found in the <a href="https://github.com/common-workflow-library/bio-cwl-tools/blob/release/subread/featureCounts.cwl" class="external-link">GitHub
 repo</a>.</p>
@@ -2040,7 +2040,7 @@ <h3 class="callout-title">Add the featureCounts tool to the workflow 🌶🌶</h
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Hint: Feature Counts Workflow Step </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>Use the <code>run</code> field to add the <code>featureCounts</code>
 tool as a step in the workflow.</p>
@@ -2053,7 +2053,7 @@ <h4 class="accordion-header" id="headingHint1"> Hint: Feature Counts Workflow St
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Hint: Upgrade RAM </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
 <div class="accordion-body">
 <p>Use a <code>requirements</code> entry with
 <code>ResourceRequirement</code> to allocate a <code>ramMin</code> of
@@ -2067,7 +2067,7 @@ <h4 class="accordion-header" id="headingHint2"> Hint: Upgrade RAM </h4>
 <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"> Solution: workflow_3.yml (Click to expand) </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="cb1">
 <h3 class="code-label">YAML<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -2165,7 +2165,7 @@ <h3 class="code-label">YAML<i aria-hidden="true" data-feather="chevron-left"></i
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler1" aria-expanded="false" aria-controls="collapseSpoiler1">
   <h3 class="accordion-header" id="headingSpoiler1">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> workflow_input_3.yml (Click to expand) </h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb2">
 <h3 class="code-label">YAML<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -2229,7 +2229,7 @@ <h3 class="callout-title">Key Points</h3>
  -->
 </section></section><section id="aio-addendum-01-debug"><p>Content from <a href="addendum-01-debug.html">Debugging Workflows</a></p>
 <hr>
-<p>Last updated on 2024-12-03 |
+<p>Last updated on 2024-12-10 |
 
         <a href="https://github.com/__USERNAME__/__PROJECT__/edit/main/episodes/addendum-01-debug.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
@@ -2320,7 +2320,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler1" aria-expanded="false" aria-controls="collapseSpoiler1">
   <h3 class="accordion-header" id="headingSpoiler1">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> Show details </h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
 <div class="accordion-body">
 <pre><code>ERROR Tool definition failed validation:
 while scanning for the next token
@@ -2394,7 +2394,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler2" aria-expanded="false" aria-controls="collapseSpoiler2">
   <h3 class="accordion-header" id="headingSpoiler2">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> CWLTOOL VALIDATE ERROR MESSAGE </h3>
 </button>
-<div id="collapseSpoiler2" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler2" aria-labelledby="headingSpoiler2">
+<div id="collapseSpoiler2" class="accordion-collapse collapse" aria-labelledby="headingSpoiler2" data-bs-parent="#accordionSpoiler2">
 <div class="accordion-body">
 <pre><code>ERROR Tool definition failed validation:
 rna_seq_workflow_fieldname_fail.cwl:1:1:   Object `rna_seq_workflow_fieldname_fail.cwl` is not valid
@@ -2486,7 +2486,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler3" aria-expanded="false" aria-controls="collapseSpoiler3">
   <h3 class="accordion-header" id="headingSpoiler3">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> CWLTOOL VALIDATE ERROR MESSAGE </h3>
 </button>
-<div id="collapseSpoiler3" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler3" aria-labelledby="headingSpoiler3">
+<div id="collapseSpoiler3" class="accordion-collapse collapse" aria-labelledby="headingSpoiler3" data-bs-parent="#accordionSpoiler3">
 <div class="accordion-body">
 <pre><code>ERROR Tool definition failed validation:
 rna_seq_workflow_varname_fail.cwl:8:1:  checking field `steps`
@@ -2608,7 +2608,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler4" aria-expanded="false" aria-controls="collapseSpoiler4">
   <h3 class="accordion-header" id="headingSpoiler4">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> Incompatible type cwltool error message </h3>
 </button>
-<div id="collapseSpoiler4" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler4" aria-labelledby="headingSpoiler4">
+<div id="collapseSpoiler4" class="accordion-collapse collapse" aria-labelledby="headingSpoiler4" data-bs-parent="#accordionSpoiler4">
 <div class="accordion-body">
 <pre><code>rna_seq_workflow_type_fail.cwl:5:3:   Source 'rna_reads_fruitfly' of type "int" is incompatible
 rna_seq_workflow_type_fail.cwl:12:7:   with sink 'reads_file' of type "File"
@@ -2710,7 +2710,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler5" aria-expanded="false" aria-controls="collapseSpoiler5">
   <h3 class="accordion-header" id="headingSpoiler5">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> Incompatible format error message </h3>
 </button>
-<div id="collapseSpoiler5" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler5" aria-labelledby="headingSpoiler5">
+<div id="collapseSpoiler5" class="accordion-collapse collapse" aria-labelledby="headingSpoiler5" data-bs-parent="#accordionSpoiler5">
 <div class="accordion-body">
 <pre><code>ERROR Exception on step 'mapping_reads'
 ERROR [step mapping_reads] Cannot make job: Expected value of 'ForwardReads' to have format http://edamontology.org/format_1930 but
@@ -2732,7 +2732,7 @@ <h3 class="accordion-header" id="headingSpoiler5">  <div class="note-square"><i
  -->
 </section></section><section id="aio-more_info"><p>Content from <a href="more_info.html">More Information</a></p>
 <hr>
-<p>Last updated on 2024-12-03 |
+<p>Last updated on 2024-12-10 |
 
         <a href="https://github.com/__USERNAME__/__PROJECT__/edit/main/episodes/more_info.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <div class="text-end">
@@ -2804,8 +2804,8 @@ <h3 class="accordion-header" id="headingSpoiler5">  <div class="note-square"><i
   "url": "https://__USERNAME__.github.io/__PROJECT__/aio.html",
   "identifier": "https://__USERNAME__.github.io/__PROJECT__/aio.html",
   "dateCreated": "2024-04-29",
-  "dateModified": "2024-12-03",
-  "datePublished": "2024-12-03"
+  "dateModified": "2024-12-10",
+  "datePublished": "2024-12-10"
 }
 
   </script><script>
diff --git a/images.html b/images.html
index 955325b..22c806f 100644
--- a/images.html
+++ b/images.html
@@ -471,8 +471,8 @@ <h3 id="03-dependency_graphs-figure-5">Figure 5</h3>
   "url": "https://__USERNAME__.github.io/__PROJECT__/images.html",
   "identifier": "https://__USERNAME__.github.io/__PROJECT__/images.html",
   "dateCreated": "2024-04-29",
-  "dateModified": "2024-12-03",
-  "datePublished": "2024-12-03"
+  "dateModified": "2024-12-10",
+  "datePublished": "2024-12-10"
 }
 
   </script><script>
diff --git a/index.html b/index.html
index 0854705..b956138 100644
--- a/index.html
+++ b/index.html
@@ -1304,8 +1304,8 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
   "url": "https://__USERNAME__.github.io/__PROJECT__/index.html",
   "identifier": "https://__USERNAME__.github.io/__PROJECT__/index.html",
   "dateCreated": "2024-04-29",
-  "dateModified": "2024-12-03",
-  "datePublished": "2024-12-03"
+  "dateModified": "2024-12-10",
+  "datePublished": "2024-12-10"
 }
 
   </script><script>
diff --git a/instructor-notes.html b/instructor-notes.html
index 2debe8e..faa49df 100644
--- a/instructor-notes.html
+++ b/instructor-notes.html
@@ -420,8 +420,8 @@ <h1>Instructor Notes</h1>
   "url": "https://__USERNAME__.github.io/__PROJECT__/instructor-notes.html",
   "identifier": "https://__USERNAME__.github.io/__PROJECT__/instructor-notes.html",
   "dateCreated": "2024-04-29",
-  "dateModified": "2024-12-03",
-  "datePublished": "2024-12-03"
+  "dateModified": "2024-12-10",
+  "datePublished": "2024-12-10"
 }
 
   </script><script>
diff --git a/instructor/01-introduction.html b/instructor/01-introduction.html
index b64ecf9..2172162 100644
--- a/instructor/01-introduction.html
+++ b/instructor/01-introduction.html
@@ -330,7 +330,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Introduction</h1>
-        <p>Last updated on 2024-12-03 |
+        <p>Last updated on 2024-12-10 |
 
         <a href="https://github.com/__USERNAME__/__PROJECT__/edit/main/episodes/01-introduction.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 
@@ -640,8 +640,8 @@ <h3 class="callout-title">Key Points</h3>
   "url": "https://__USERNAME__.github.io/__PROJECT__/instructor/01-introduction.html",
   "identifier": "https://__USERNAME__.github.io/__PROJECT__/instructor/01-introduction.html",
   "dateCreated": "2024-04-29",
-  "dateModified": "2024-12-03",
-  "datePublished": "2024-12-03"
+  "dateModified": "2024-12-10",
+  "datePublished": "2024-12-10"
 }
 
   </script><script>
diff --git a/instructor/02-shell_to_cwl.html b/instructor/02-shell_to_cwl.html
index ab69fcf..bd4261f 100644
--- a/instructor/02-shell_to_cwl.html
+++ b/instructor/02-shell_to_cwl.html
@@ -326,7 +326,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>CWL and Shell Tools</h1>
-        <p>Last updated on 2024-12-03 |
+        <p>Last updated on 2024-12-10 |
 
         <a href="https://github.com/__USERNAME__/__PROJECT__/edit/main/episodes/02-shell_to_cwl.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 
@@ -445,7 +445,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler1" aria-expanded="false" aria-controls="collapseSpoiler1">
   <h3 class="accordion-header" id="headingSpoiler1">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> Tool Output </h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
 <div class="accordion-body">
 <pre class="text"><code>INFO Resolved 'echo.cwl' to 'file:///.../echo.cwl'
 INFO [job echo.cwl] /private/tmp/docker_tmprm65mucw$ echo \
@@ -560,7 +560,7 @@ <h3 class="callout-title">Changing the output string 🌶</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>To change the text on the command line, you only have to change the
 text in the <code>hello_world.yml</code> file.</p>
@@ -591,7 +591,7 @@ <h3 class="callout-title">Updating the arguments 🌶🌶</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">
 <div class="codewrapper sourceCode" id="cb10">
 <h3 class="code-label">YAML<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -625,7 +625,7 @@ <h3 class="callout-title">Redirecting cwltool stdout and stderr 🌶🌶</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Hint: Redirecting CLI stdout and stderr </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>Use the redirectors <code>1&gt;</code> and <code>2&gt;</code> to
 redirect stdout and stderr to different files respectively</p>
@@ -638,7 +638,7 @@ <h4 class="accordion-header" id="headingHint1"> Hint: Redirecting CLI stdout and
 <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="cb11">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -673,7 +673,7 @@ <h3 class="callout-title">Specifying the stdout of the tool as a CWL output 🌶
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Hint - stdout output binding </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
 <div class="accordion-body">
 <p>Copy the ‘outputBinding’ from the tutorial ‘verbatim’.</p>
 <p>Your output key should look like this</p>
@@ -697,7 +697,7 @@ <h3 class="code-label">YAML<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="#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="cb13">
 <h3 class="code-label">YAML<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -941,7 +941,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler2" aria-expanded="false" aria-controls="collapseSpoiler2">
   <h3 class="accordion-header" id="headingSpoiler2">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> Console Outputs </h3>
 </button>
-<div id="collapseSpoiler2" class="accordion-collapse collapse" aria-labelledby="headingSpoiler2" data-bs-parent="#accordionSpoiler2">
+<div id="collapseSpoiler2" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler2" aria-labelledby="headingSpoiler2">
 <div class="accordion-body">
 <pre><code>...
 Analysis complete for GSM461177_2_subsampled.fastqsanger
@@ -1001,7 +1001,7 @@ <h3 class="callout-title">Directly embed a Commandlinetool into a file 🌶🌶<
 <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">
 <p>The <code>run</code> field in the step can be replaced with the
 <code>CommandLineTool</code> definition.</p>
@@ -1048,7 +1048,7 @@ <h3 class="callout-title">Embedding Tool Descriptions</h3>
 <button class="accordion-button instructor-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseInstructor1" aria-expanded="false" aria-controls="collapseInstructor1">
   <h3 class="accordion-header" id="headingInstructor1">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="edit-2"></i></div> Exercise </h3>
 </button>
-<div id="collapseInstructor1" class="accordion-collapse collapse" aria-labelledby="headingInstructor1" data-bs-parent="#accordionInstructor1">
+<div id="collapseInstructor1" class="accordion-collapse collapse" data-bs-parent="#accordionInstructor1" aria-labelledby="headingInstructor1">
 <div class="accordion-body">
 <p>Needs some exercises?</p>
 <ul><li>Ask the students to get some information from each report generated
@@ -1138,8 +1138,8 @@ <h3 class="callout-title">Key Points</h3>
   "url": "https://__USERNAME__.github.io/__PROJECT__/instructor/02-shell_to_cwl.html",
   "identifier": "https://__USERNAME__.github.io/__PROJECT__/instructor/02-shell_to_cwl.html",
   "dateCreated": "2024-04-29",
-  "dateModified": "2024-12-03",
-  "datePublished": "2024-12-03"
+  "dateModified": "2024-12-10",
+  "datePublished": "2024-12-10"
 }
 
   </script><script>
diff --git a/instructor/03-dependency_graphs.html b/instructor/03-dependency_graphs.html
index 4d98587..538ca34 100644
--- a/instructor/03-dependency_graphs.html
+++ b/instructor/03-dependency_graphs.html
@@ -327,7 +327,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Developing Multi-Step Workflows</h1>
-        <p>Last updated on 2024-12-03 |
+        <p>Last updated on 2024-12-10 |
 
         <a href="https://github.com/__USERNAME__/__PROJECT__/edit/main/episodes/03-dependency_graphs.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 
@@ -405,7 +405,7 @@ <h3 class="callout-title">Naming steps</h3>
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler1" aria-expanded="false" aria-controls="collapseSpoiler1">
   <h3 class="accordion-header" id="headingSpoiler1">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> rna_seq_workflow_2.cwl (Click to expand) </h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb1">
 <h3 class="code-label">YAML<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -550,7 +550,7 @@ <h3 class="callout-title">Is this a valid workflow? 🌶</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="cb2">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -584,7 +584,7 @@ <h3 class="callout-title">Should we be concerned about this warning 🌶🌶🌶
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <p>In this case, the outputs of the mapping step may instead either be
 just one file, OR an array of files.</p>
@@ -603,7 +603,7 @@ <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler2" aria-expanded="false" aria-controls="collapseSpoiler2">
   <h3 class="accordion-header" id="headingSpoiler2">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> workflow_input_2.yml (Click to expand) </h3>
 </button>
-<div id="collapseSpoiler2" class="accordion-collapse collapse" aria-labelledby="headingSpoiler2" data-bs-parent="#accordionSpoiler2">
+<div id="collapseSpoiler2" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler2" aria-labelledby="headingSpoiler2">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb4">
 <h3 class="code-label">YAML<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -652,7 +652,7 @@ <h3 class="callout-title">Challenge: Draw the workflow 🌶</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>To find out how the inputs and the steps are connected to each other,
 look at the <code>in</code> field of the different steps.</p>
@@ -728,7 +728,7 @@ <h3 class="callout-title">Push your workflow to GitHub 🌶</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"> Git add / commit / push </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
 <div class="accordion-body">
 <p>Your solution might look like this</p>
 <div class="codewrapper sourceCode" id="cb6">
@@ -884,8 +884,8 @@ <h3 class="callout-title">Key Points</h3>
   "url": "https://__USERNAME__.github.io/__PROJECT__/instructor/03-dependency_graphs.html",
   "identifier": "https://__USERNAME__.github.io/__PROJECT__/instructor/03-dependency_graphs.html",
   "dateCreated": "2024-04-29",
-  "dateModified": "2024-12-03",
-  "datePublished": "2024-12-03"
+  "dateModified": "2024-12-10",
+  "datePublished": "2024-12-10"
 }
 
   </script><script>
diff --git a/instructor/04-reusing_tools.html b/instructor/04-reusing_tools.html
index d7eafb7..0aa8e2f 100644
--- a/instructor/04-reusing_tools.html
+++ b/instructor/04-reusing_tools.html
@@ -326,7 +326,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Resources for Reusing Tools and Scripts</h1>
-        <p>Last updated on 2024-12-03 |
+        <p>Last updated on 2024-12-10 |
 
         <a href="https://github.com/__USERNAME__/__PROJECT__/edit/main/episodes/04-reusing_tools.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 
@@ -392,7 +392,7 @@ <h3 class="callout-title">Find the featureCounts tool in the bio-cwl-tools libra
 <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 <code>featureCounts</code> CWL document can be found in the <a href="https://github.com/common-workflow-library/bio-cwl-tools/blob/release/subread/featureCounts.cwl" class="external-link">GitHub
 repo</a>.</p>
@@ -438,7 +438,7 @@ <h3 class="callout-title">Add the featureCounts tool to the workflow 🌶🌶</h
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Hint: Feature Counts Workflow Step </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>Use the <code>run</code> field to add the <code>featureCounts</code>
 tool as a step in the workflow.</p>
@@ -451,7 +451,7 @@ <h4 class="accordion-header" id="headingHint1"> Hint: Feature Counts Workflow St
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Hint: Upgrade RAM </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
 <div class="accordion-body">
 <p>Use a <code>requirements</code> entry with
 <code>ResourceRequirement</code> to allocate a <code>ramMin</code> of
@@ -465,7 +465,7 @@ <h4 class="accordion-header" id="headingHint2"> Hint: Upgrade RAM </h4>
 <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"> Solution: workflow_3.yml (Click to expand) </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="cb1">
 <h3 class="code-label">YAML<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -561,7 +561,7 @@ <h3 class="code-label">YAML<i aria-hidden="true" data-feather="chevron-left"></i
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler1" aria-expanded="false" aria-controls="collapseSpoiler1">
   <h3 class="accordion-header" id="headingSpoiler1">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> workflow_input_3.yml (Click to expand) </h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb2">
 <h3 class="code-label">YAML<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -679,8 +679,8 @@ <h3 class="callout-title">Key Points</h3>
   "url": "https://__USERNAME__.github.io/__PROJECT__/instructor/04-reusing_tools.html",
   "identifier": "https://__USERNAME__.github.io/__PROJECT__/instructor/04-reusing_tools.html",
   "dateCreated": "2024-04-29",
-  "dateModified": "2024-12-03",
-  "datePublished": "2024-12-03"
+  "dateModified": "2024-12-10",
+  "datePublished": "2024-12-10"
 }
 
   </script><script>
diff --git a/instructor/404.html b/instructor/404.html
index 5dbf2fd..1d1f367 100644
--- a/instructor/404.html
+++ b/instructor/404.html
@@ -375,8 +375,8 @@ <h1>Page not found</h1>
   "url": "https://__USERNAME__.github.io/__PROJECT__/instructor/404.html",
   "identifier": "https://__USERNAME__.github.io/__PROJECT__/instructor/404.html",
   "dateCreated": "2024-04-29",
-  "dateModified": "2024-12-03",
-  "datePublished": "2024-12-03"
+  "dateModified": "2024-12-10",
+  "datePublished": "2024-12-10"
 }
 
   </script><script>
diff --git a/instructor/CODE_OF_CONDUCT.html b/instructor/CODE_OF_CONDUCT.html
index 787e383..1b4e4d8 100644
--- a/instructor/CODE_OF_CONDUCT.html
+++ b/instructor/CODE_OF_CONDUCT.html
@@ -313,7 +313,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Contributor Code of Conduct</h1>
-        <p>Last updated on 2024-12-03 |
+        <p>Last updated on 2024-12-10 |
 
         <a href="https://github.com/__USERNAME__/__PROJECT__/edit/main/CODE_OF_CONDUCT.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 
@@ -408,8 +408,8 @@ <h1>Contributor Code of Conduct</h1>
   "url": "https://__USERNAME__.github.io/__PROJECT__/instructor/CODE_OF_CONDUCT.html",
   "identifier": "https://__USERNAME__.github.io/__PROJECT__/instructor/CODE_OF_CONDUCT.html",
   "dateCreated": "2024-04-29",
-  "dateModified": "2024-12-03",
-  "datePublished": "2024-12-03"
+  "dateModified": "2024-12-10",
+  "datePublished": "2024-12-10"
 }
 
   </script><script>
diff --git a/instructor/LICENSE.html b/instructor/LICENSE.html
index d604f10..bc6272e 100644
--- a/instructor/LICENSE.html
+++ b/instructor/LICENSE.html
@@ -313,7 +313,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Licenses</h1>
-        <p>Last updated on 2024-12-03 |
+        <p>Last updated on 2024-12-10 |
 
         <a href="https://github.com/__USERNAME__/__PROJECT__/edit/main/LICENSE.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 
@@ -439,8 +439,8 @@ <h1>Licenses</h1>
   "url": "https://__USERNAME__.github.io/__PROJECT__/instructor/LICENSE.html",
   "identifier": "https://__USERNAME__.github.io/__PROJECT__/instructor/LICENSE.html",
   "dateCreated": "2024-04-29",
-  "dateModified": "2024-12-03",
-  "datePublished": "2024-12-03"
+  "dateModified": "2024-12-10",
+  "datePublished": "2024-12-10"
 }
 
   </script><script>
diff --git a/instructor/addendum-01-debug.html b/instructor/addendum-01-debug.html
index 6937741..477283f 100644
--- a/instructor/addendum-01-debug.html
+++ b/instructor/addendum-01-debug.html
@@ -329,7 +329,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>Debugging Workflows</h1>
-        <p>Last updated on 2024-12-03 |
+        <p>Last updated on 2024-12-10 |
 
         <a href="https://github.com/__USERNAME__/__PROJECT__/edit/main/episodes/addendum-01-debug.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 
@@ -420,7 +420,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler1" aria-expanded="false" aria-controls="collapseSpoiler1">
   <h3 class="accordion-header" id="headingSpoiler1">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> Show details </h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
 <div class="accordion-body">
 <pre><code>ERROR Tool definition failed validation:
 while scanning for the next token
@@ -492,7 +492,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler2" aria-expanded="false" aria-controls="collapseSpoiler2">
   <h3 class="accordion-header" id="headingSpoiler2">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> CWLTOOL VALIDATE ERROR MESSAGE </h3>
 </button>
-<div id="collapseSpoiler2" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler2" aria-labelledby="headingSpoiler2">
+<div id="collapseSpoiler2" class="accordion-collapse collapse" aria-labelledby="headingSpoiler2" data-bs-parent="#accordionSpoiler2">
 <div class="accordion-body">
 <pre><code>ERROR Tool definition failed validation:
 rna_seq_workflow_fieldname_fail.cwl:1:1:   Object `rna_seq_workflow_fieldname_fail.cwl` is not valid
@@ -582,7 +582,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler3" aria-expanded="false" aria-controls="collapseSpoiler3">
   <h3 class="accordion-header" id="headingSpoiler3">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> CWLTOOL VALIDATE ERROR MESSAGE </h3>
 </button>
-<div id="collapseSpoiler3" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler3" aria-labelledby="headingSpoiler3">
+<div id="collapseSpoiler3" class="accordion-collapse collapse" aria-labelledby="headingSpoiler3" data-bs-parent="#accordionSpoiler3">
 <div class="accordion-body">
 <pre><code>ERROR Tool definition failed validation:
 rna_seq_workflow_varname_fail.cwl:8:1:  checking field `steps`
@@ -700,7 +700,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler4" aria-expanded="false" aria-controls="collapseSpoiler4">
   <h3 class="accordion-header" id="headingSpoiler4">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> Incompatible type cwltool error message </h3>
 </button>
-<div id="collapseSpoiler4" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler4" aria-labelledby="headingSpoiler4">
+<div id="collapseSpoiler4" class="accordion-collapse collapse" aria-labelledby="headingSpoiler4" data-bs-parent="#accordionSpoiler4">
 <div class="accordion-body">
 <pre><code>rna_seq_workflow_type_fail.cwl:5:3:   Source 'rna_reads_fruitfly' of type "int" is incompatible
 rna_seq_workflow_type_fail.cwl:12:7:   with sink 'reads_file' of type "File"
@@ -800,7 +800,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler5" aria-expanded="false" aria-controls="collapseSpoiler5">
   <h3 class="accordion-header" id="headingSpoiler5">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> Incompatible format error message </h3>
 </button>
-<div id="collapseSpoiler5" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler5" aria-labelledby="headingSpoiler5">
+<div id="collapseSpoiler5" class="accordion-collapse collapse" aria-labelledby="headingSpoiler5" data-bs-parent="#accordionSpoiler5">
 <div class="accordion-body">
 <pre><code>ERROR Exception on step 'mapping_reads'
 ERROR [step mapping_reads] Cannot make job: Expected value of 'ForwardReads' to have format http://edamontology.org/format_1930 but
@@ -878,8 +878,8 @@ <h3 class="accordion-header" id="headingSpoiler5">  <div class="note-square"><i
   "url": "https://__USERNAME__.github.io/__PROJECT__/instructor/addendum-01-debug.html",
   "identifier": "https://__USERNAME__.github.io/__PROJECT__/instructor/addendum-01-debug.html",
   "dateCreated": "2024-04-29",
-  "dateModified": "2024-12-03",
-  "datePublished": "2024-12-03"
+  "dateModified": "2024-12-10",
+  "datePublished": "2024-12-10"
 }
 
   </script><script>
diff --git a/instructor/aio.html b/instructor/aio.html
index 585c873..4473428 100644
--- a/instructor/aio.html
+++ b/instructor/aio.html
@@ -366,7 +366,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
         
 <section id="aio-01-introduction"><p>Content from <a href="01-introduction.html">Introduction</a></p>
 <hr>
-<p>Last updated on 2024-12-03 |
+<p>Last updated on 2024-12-10 |
 
         <a href="https://github.com/__USERNAME__/__PROJECT__/edit/main/episodes/01-introduction.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 0 minutes</p>
@@ -654,7 +654,7 @@ <h3 class="callout-title">Key Points</h3>
 </ol>
 </div></section><section id="aio-02-shell_to_cwl"><p>Content from <a href="02-shell_to_cwl.html">CWL and Shell Tools</a></p>
 <hr>
-<p>Last updated on 2024-12-03 |
+<p>Last updated on 2024-12-10 |
 
         <a href="https://github.com/__USERNAME__/__PROJECT__/edit/main/episodes/02-shell_to_cwl.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 0 minutes</p>
@@ -772,7 +772,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler1" aria-expanded="false" aria-controls="collapseSpoiler1">
   <h3 class="accordion-header" id="headingSpoiler1">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> Tool Output </h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
 <div class="accordion-body">
 <pre class="text"><code>INFO Resolved 'echo.cwl' to 'file:///.../echo.cwl'
 INFO [job echo.cwl] /private/tmp/docker_tmprm65mucw$ echo \
@@ -892,7 +892,7 @@ <h3 class="callout-title">Changing the output string 🌶</h3>
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>To change the text on the command line, you only have to change the
 text in the <code>hello_world.yml</code> file.</p>
@@ -923,7 +923,7 @@ <h3 class="callout-title">Updating the arguments 🌶🌶</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">
 <div class="codewrapper sourceCode" id="cb10">
 <h3 class="code-label">YAML<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -957,7 +957,7 @@ <h3 class="callout-title">Redirecting cwltool stdout and stderr 🌶🌶</h3>
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Hint: Redirecting CLI stdout and stderr </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>Use the redirectors <code>1&gt;</code> and <code>2&gt;</code> to
 redirect stdout and stderr to different files respectively</p>
@@ -970,7 +970,7 @@ <h4 class="accordion-header" id="headingHint1"> Hint: Redirecting CLI stdout and
 <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="cb11">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1005,7 +1005,7 @@ <h3 class="callout-title">Specifying the stdout of the tool as a CWL output 🌶
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Hint - stdout output binding </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
 <div class="accordion-body">
 <p>Copy the ‘outputBinding’ from the tutorial ‘verbatim’.</p>
 <p>Your output key should look like this</p>
@@ -1029,7 +1029,7 @@ <h3 class="code-label">YAML<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="#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="cb13">
 <h3 class="code-label">YAML<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1284,7 +1284,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler2" aria-expanded="false" aria-controls="collapseSpoiler2">
   <h3 class="accordion-header" id="headingSpoiler2">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> Console Outputs </h3>
 </button>
-<div id="collapseSpoiler2" class="accordion-collapse collapse" aria-labelledby="headingSpoiler2" data-bs-parent="#accordionSpoiler2">
+<div id="collapseSpoiler2" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler2" aria-labelledby="headingSpoiler2">
 <div class="accordion-body">
 <pre><code>...
 Analysis complete for GSM461177_2_subsampled.fastqsanger
@@ -1345,7 +1345,7 @@ <h3 class="callout-title">Directly embed a Commandlinetool into a file 🌶🌶<
 <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">
 <p>The <code>run</code> field in the step can be replaced with the
 <code>CommandLineTool</code> definition.</p>
@@ -1392,7 +1392,7 @@ <h3 class="callout-title">Embedding Tool Descriptions</h3>
 <button class="accordion-button instructor-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseInstructor1" aria-expanded="false" aria-controls="collapseInstructor1">
   <h3 class="accordion-header" id="headingInstructor1">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="edit-2"></i></div> Exercise </h3>
 </button>
-<div id="collapseInstructor1" class="accordion-collapse collapse" aria-labelledby="headingInstructor1" data-bs-parent="#accordionInstructor1">
+<div id="collapseInstructor1" class="accordion-collapse collapse" data-bs-parent="#accordionInstructor1" aria-labelledby="headingInstructor1">
 <div class="accordion-body">
 <p>Needs some exercises?</p>
 <ul>
@@ -1430,7 +1430,7 @@ <h3 class="callout-title">Key Points</h3>
 </div>
 </section></section><section id="aio-03-dependency_graphs"><p>Content from <a href="03-dependency_graphs.html">Developing Multi-Step Workflows</a></p>
 <hr>
-<p>Last updated on 2024-12-03 |
+<p>Last updated on 2024-12-10 |
 
         <a href="https://github.com/__USERNAME__/__PROJECT__/edit/main/episodes/03-dependency_graphs.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 0 minutes</p>
@@ -1507,7 +1507,7 @@ <h3 class="callout-title">Naming steps</h3>
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler1" aria-expanded="false" aria-controls="collapseSpoiler1">
   <h3 class="accordion-header" id="headingSpoiler1">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> rna_seq_workflow_2.cwl (Click to expand) </h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb1">
 <h3 class="code-label">YAML<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1654,7 +1654,7 @@ <h3 class="callout-title">Is this a valid workflow? 🌶</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="cb2">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1688,7 +1688,7 @@ <h3 class="callout-title">Should we be concerned about this warning 🌶🌶🌶
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
 <div class="accordion-body">
 <p>In this case, the outputs of the mapping step may instead either be
 just one file, OR an array of files.</p>
@@ -1709,7 +1709,7 @@ <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler2" aria-expanded="false" aria-controls="collapseSpoiler2">
   <h3 class="accordion-header" id="headingSpoiler2">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> workflow_input_2.yml (Click to expand) </h3>
 </button>
-<div id="collapseSpoiler2" class="accordion-collapse collapse" aria-labelledby="headingSpoiler2" data-bs-parent="#accordionSpoiler2">
+<div id="collapseSpoiler2" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler2" aria-labelledby="headingSpoiler2">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb4">
 <h3 class="code-label">YAML<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1759,7 +1759,7 @@ <h3 class="callout-title">Challenge: Draw the workflow 🌶</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>To find out how the inputs and the steps are connected to each other,
 look at the <code>in</code> field of the different steps.</p>
@@ -1841,7 +1841,7 @@ <h3 class="callout-title">Push your workflow to GitHub 🌶</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"> Git add / commit / push </h4>
 </button>
-<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
 <div class="accordion-body">
 <p>Your solution might look like this</p>
 <div class="codewrapper sourceCode" id="cb6">
@@ -1946,7 +1946,7 @@ <h3 class="callout-title">Key Points</h3>
 </div>
 </section></section><section id="aio-04-reusing_tools"><p>Content from <a href="04-reusing_tools.html">Resources for Reusing Tools and Scripts</a></p>
 <hr>
-<p>Last updated on 2024-12-03 |
+<p>Last updated on 2024-12-10 |
 
         <a href="https://github.com/__USERNAME__/__PROJECT__/edit/main/episodes/04-reusing_tools.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 0 minutes</p>
@@ -2013,7 +2013,7 @@ <h3 class="callout-title">Find the featureCounts tool in the bio-cwl-tools libra
 <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 <code>featureCounts</code> CWL document can be found in the <a href="https://github.com/common-workflow-library/bio-cwl-tools/blob/release/subread/featureCounts.cwl" class="external-link">GitHub
 repo</a>.</p>
@@ -2060,7 +2060,7 @@ <h3 class="callout-title">Add the featureCounts tool to the workflow 🌶🌶</h
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint1" aria-expanded="false" aria-controls="collapseHint1">
   <h4 class="accordion-header" id="headingHint1"> Hint: Feature Counts Workflow Step </h4>
 </button>
-<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
 <div class="accordion-body">
 <p>Use the <code>run</code> field to add the <code>featureCounts</code>
 tool as a step in the workflow.</p>
@@ -2073,7 +2073,7 @@ <h4 class="accordion-header" id="headingHint1"> Hint: Feature Counts Workflow St
 <button class="accordion-button hint-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseHint2" aria-expanded="false" aria-controls="collapseHint2">
   <h4 class="accordion-header" id="headingHint2"> Hint: Upgrade RAM </h4>
 </button>
-<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
 <div class="accordion-body">
 <p>Use a <code>requirements</code> entry with
 <code>ResourceRequirement</code> to allocate a <code>ramMin</code> of
@@ -2087,7 +2087,7 @@ <h4 class="accordion-header" id="headingHint2"> Hint: Upgrade RAM </h4>
 <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"> Solution: workflow_3.yml (Click to expand) </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="cb1">
 <h3 class="code-label">YAML<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -2185,7 +2185,7 @@ <h3 class="code-label">YAML<i aria-hidden="true" data-feather="chevron-left"></i
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler1" aria-expanded="false" aria-controls="collapseSpoiler1">
   <h3 class="accordion-header" id="headingSpoiler1">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> workflow_input_3.yml (Click to expand) </h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb2">
 <h3 class="code-label">YAML<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -2249,7 +2249,7 @@ <h3 class="callout-title">Key Points</h3>
  -->
 </section></section><section id="aio-addendum-01-debug"><p>Content from <a href="addendum-01-debug.html">Debugging Workflows</a></p>
 <hr>
-<p>Last updated on 2024-12-03 |
+<p>Last updated on 2024-12-10 |
 
         <a href="https://github.com/__USERNAME__/__PROJECT__/edit/main/episodes/addendum-01-debug.Rmd" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 0 minutes</p>
@@ -2341,7 +2341,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler1" aria-expanded="false" aria-controls="collapseSpoiler1">
   <h3 class="accordion-header" id="headingSpoiler1">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> Show details </h3>
 </button>
-<div id="collapseSpoiler1" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler1" aria-labelledby="headingSpoiler1">
+<div id="collapseSpoiler1" class="accordion-collapse collapse" aria-labelledby="headingSpoiler1" data-bs-parent="#accordionSpoiler1">
 <div class="accordion-body">
 <pre><code>ERROR Tool definition failed validation:
 while scanning for the next token
@@ -2415,7 +2415,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler2" aria-expanded="false" aria-controls="collapseSpoiler2">
   <h3 class="accordion-header" id="headingSpoiler2">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> CWLTOOL VALIDATE ERROR MESSAGE </h3>
 </button>
-<div id="collapseSpoiler2" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler2" aria-labelledby="headingSpoiler2">
+<div id="collapseSpoiler2" class="accordion-collapse collapse" aria-labelledby="headingSpoiler2" data-bs-parent="#accordionSpoiler2">
 <div class="accordion-body">
 <pre><code>ERROR Tool definition failed validation:
 rna_seq_workflow_fieldname_fail.cwl:1:1:   Object `rna_seq_workflow_fieldname_fail.cwl` is not valid
@@ -2507,7 +2507,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler3" aria-expanded="false" aria-controls="collapseSpoiler3">
   <h3 class="accordion-header" id="headingSpoiler3">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> CWLTOOL VALIDATE ERROR MESSAGE </h3>
 </button>
-<div id="collapseSpoiler3" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler3" aria-labelledby="headingSpoiler3">
+<div id="collapseSpoiler3" class="accordion-collapse collapse" aria-labelledby="headingSpoiler3" data-bs-parent="#accordionSpoiler3">
 <div class="accordion-body">
 <pre><code>ERROR Tool definition failed validation:
 rna_seq_workflow_varname_fail.cwl:8:1:  checking field `steps`
@@ -2629,7 +2629,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler4" aria-expanded="false" aria-controls="collapseSpoiler4">
   <h3 class="accordion-header" id="headingSpoiler4">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> Incompatible type cwltool error message </h3>
 </button>
-<div id="collapseSpoiler4" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler4" aria-labelledby="headingSpoiler4">
+<div id="collapseSpoiler4" class="accordion-collapse collapse" aria-labelledby="headingSpoiler4" data-bs-parent="#accordionSpoiler4">
 <div class="accordion-body">
 <pre><code>rna_seq_workflow_type_fail.cwl:5:3:   Source 'rna_reads_fruitfly' of type "int" is incompatible
 rna_seq_workflow_type_fail.cwl:12:7:   with sink 'reads_file' of type "File"
@@ -2731,7 +2731,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <button class="accordion-button spoiler-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSpoiler5" aria-expanded="false" aria-controls="collapseSpoiler5">
   <h3 class="accordion-header" id="headingSpoiler5">  <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div> Incompatible format error message </h3>
 </button>
-<div id="collapseSpoiler5" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler5" aria-labelledby="headingSpoiler5">
+<div id="collapseSpoiler5" class="accordion-collapse collapse" aria-labelledby="headingSpoiler5" data-bs-parent="#accordionSpoiler5">
 <div class="accordion-body">
 <pre><code>ERROR Exception on step 'mapping_reads'
 ERROR [step mapping_reads] Cannot make job: Expected value of 'ForwardReads' to have format http://edamontology.org/format_1930 but
@@ -2753,7 +2753,7 @@ <h3 class="accordion-header" id="headingSpoiler5">  <div class="note-square"><i
  -->
 </section></section><section id="aio-more_info"><p>Content from <a href="more_info.html">More Information</a></p>
 <hr>
-<p>Last updated on 2024-12-03 |
+<p>Last updated on 2024-12-10 |
 
         <a href="https://github.com/__USERNAME__/__PROJECT__/edit/main/episodes/more_info.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 <p>Estimated time: <i aria-hidden="true" data-feather="clock"></i> 0 minutes</p>
@@ -2826,8 +2826,8 @@ <h3 class="accordion-header" id="headingSpoiler5">  <div class="note-square"><i
   "url": "https://__USERNAME__.github.io/__PROJECT__/instructor/aio.html",
   "identifier": "https://__USERNAME__.github.io/__PROJECT__/instructor/aio.html",
   "dateCreated": "2024-04-29",
-  "dateModified": "2024-12-03",
-  "datePublished": "2024-12-03"
+  "dateModified": "2024-12-10",
+  "datePublished": "2024-12-10"
 }
 
   </script><script>
diff --git a/instructor/images.html b/instructor/images.html
index e93da02..33e607e 100644
--- a/instructor/images.html
+++ b/instructor/images.html
@@ -471,8 +471,8 @@ <h3 id="03-dependency_graphs-figure-5">Figure 5</h3>
   "url": "https://__USERNAME__.github.io/__PROJECT__/instructor/images.html",
   "identifier": "https://__USERNAME__.github.io/__PROJECT__/instructor/images.html",
   "dateCreated": "2024-04-29",
-  "dateModified": "2024-12-03",
-  "datePublished": "2024-12-03"
+  "dateModified": "2024-12-10",
+  "datePublished": "2024-12-10"
 }
 
   </script><script>
diff --git a/instructor/index.html b/instructor/index.html
index 99d33bf..cd65c67 100644
--- a/instructor/index.html
+++ b/instructor/index.html
@@ -1368,8 +1368,8 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
   "url": "https://__USERNAME__.github.io/__PROJECT__/instructor/index.html",
   "identifier": "https://__USERNAME__.github.io/__PROJECT__/instructor/index.html",
   "dateCreated": "2024-04-29",
-  "dateModified": "2024-12-03",
-  "datePublished": "2024-12-03"
+  "dateModified": "2024-12-10",
+  "datePublished": "2024-12-10"
 }
 
   </script><script>
diff --git a/instructor/instructor-notes.html b/instructor/instructor-notes.html
index 5d5a6f5..a302f13 100644
--- a/instructor/instructor-notes.html
+++ b/instructor/instructor-notes.html
@@ -437,8 +437,8 @@ <h3 id="02-shell_to_cwl-headingInstructor1">
   "url": "https://__USERNAME__.github.io/__PROJECT__/instructor/instructor-notes.html",
   "identifier": "https://__USERNAME__.github.io/__PROJECT__/instructor/instructor-notes.html",
   "dateCreated": "2024-04-29",
-  "dateModified": "2024-12-03",
-  "datePublished": "2024-12-03"
+  "dateModified": "2024-12-10",
+  "datePublished": "2024-12-10"
 }
 
   </script><script>
diff --git a/instructor/key-points.html b/instructor/key-points.html
index f93ed26..9e79e32 100644
--- a/instructor/key-points.html
+++ b/instructor/key-points.html
@@ -448,8 +448,8 @@ <h2 class="accordion-header" id="flush-headingTwelve">
   "url": "https://__USERNAME__.github.io/__PROJECT__/instructor/key-points.html",
   "identifier": "https://__USERNAME__.github.io/__PROJECT__/instructor/key-points.html",
   "dateCreated": "2024-04-29",
-  "dateModified": "2024-12-03",
-  "datePublished": "2024-12-03"
+  "dateModified": "2024-12-10",
+  "datePublished": "2024-12-10"
 }
 
   </script><script>
diff --git a/instructor/more_info.html b/instructor/more_info.html
index 2502673..fdfa16b 100644
--- a/instructor/more_info.html
+++ b/instructor/more_info.html
@@ -317,7 +317,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>More Information</h1>
-        <p>Last updated on 2024-12-03 |
+        <p>Last updated on 2024-12-10 |
 
         <a href="https://github.com/__USERNAME__/__PROJECT__/edit/main/episodes/more_info.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 
@@ -407,8 +407,8 @@ <h1>More Information</h1>
   "url": "https://__USERNAME__.github.io/__PROJECT__/instructor/more_info.html",
   "identifier": "https://__USERNAME__.github.io/__PROJECT__/instructor/more_info.html",
   "dateCreated": "2024-04-29",
-  "dateModified": "2024-12-03",
-  "datePublished": "2024-12-03"
+  "dateModified": "2024-12-10",
+  "datePublished": "2024-12-10"
 }
 
   </script><script>
diff --git a/instructor/profiles.html b/instructor/profiles.html
index 1d51f22..5c7c8e7 100644
--- a/instructor/profiles.html
+++ b/instructor/profiles.html
@@ -350,8 +350,8 @@ <h1>Learner Profiles</h1>
   "url": "https://__USERNAME__.github.io/__PROJECT__/instructor/profiles.html",
   "identifier": "https://__USERNAME__.github.io/__PROJECT__/instructor/profiles.html",
   "dateCreated": "2024-04-29",
-  "dateModified": "2024-12-03",
-  "datePublished": "2024-12-03"
+  "dateModified": "2024-12-10",
+  "datePublished": "2024-12-10"
 }
 
   </script><script>
diff --git a/instructor/reference.html b/instructor/reference.html
index c13b0c8..2616adf 100644
--- a/instructor/reference.html
+++ b/instructor/reference.html
@@ -313,7 +313,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1></h1>
-        <p>Last updated on 2024-12-03 |
+        <p>Last updated on 2024-12-10 |
 
         <a href="https://github.com/__USERNAME__/__PROJECT__/edit/main/old_carpentries_incubator/reference.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 
@@ -391,8 +391,8 @@ <h1></h1>
   "url": "https://__USERNAME__.github.io/__PROJECT__/instructor/reference.html",
   "identifier": "https://__USERNAME__.github.io/__PROJECT__/instructor/reference.html",
   "dateCreated": "2024-04-29",
-  "dateModified": "2024-12-03",
-  "datePublished": "2024-12-03"
+  "dateModified": "2024-12-10",
+  "datePublished": "2024-12-10"
 }
 
   </script><script>
diff --git a/key-points.html b/key-points.html
index b073196..a6e35e7 100644
--- a/key-points.html
+++ b/key-points.html
@@ -448,8 +448,8 @@ <h2 class="accordion-header" id="flush-headingTwelve">
   "url": "https://__USERNAME__.github.io/__PROJECT__/key-points.html",
   "identifier": "https://__USERNAME__.github.io/__PROJECT__/key-points.html",
   "dateCreated": "2024-04-29",
-  "dateModified": "2024-12-03",
-  "datePublished": "2024-12-03"
+  "dateModified": "2024-12-10",
+  "datePublished": "2024-12-10"
 }
 
   </script><script>
diff --git a/md5sum.txt b/md5sum.txt
index 6981129..7f1cd22 100644
--- a/md5sum.txt
+++ b/md5sum.txt
@@ -1,19 +1,19 @@
 "file" "checksum" "built" "date"
-"CODE_OF_CONDUCT.md" "06f4c4289ab6bb4db4fa69f818cf24ba" "site/built/CODE_OF_CONDUCT.md" "2024-12-03"
-"LICENSE.md" "8a0a618b3207e1817844a86db497bff9" "site/built/LICENSE.md" "2024-12-03"
-"config.yaml" "75323286755b184e154f3123eb45ef38" "site/built/config.yaml" "2024-12-03"
-"index.md" "000a1a2b1e4e4f274b3dbff311b49818" "site/built/index.md" "2024-12-03"
-"links.md" "8184cf4149eafbf03ce8da8ff0778c14" "site/built/links.md" "2024-12-03"
-"episodes/01-introduction.Rmd" "d32b6b5562a66dc90d79acbf60210375" "site/built/01-introduction.md" "2024-12-03"
-"episodes/02-shell_to_cwl.Rmd" "9d08ba8ae7875dee96e8f80de70907ea" "site/built/02-shell_to_cwl.md" "2024-12-03"
-"episodes/03-dependency_graphs.Rmd" "f55a067639c7f056312d9e137fdf2ed6" "site/built/03-dependency_graphs.md" "2024-12-03"
-"episodes/04-reusing_tools.Rmd" "4a90245e02110dbb13296102d3ce75a2" "site/built/04-reusing_tools.md" "2024-12-03"
-"episodes/addendum-01-debug.Rmd" "3ce548abd8cb1934aa12b16cd62104e3" "site/built/addendum-01-debug.md" "2024-12-03"
-"episodes/more_info.md" "b97f3b7186f568f33352041b7e2449ff" "site/built/more_info.md" "2024-12-03"
-"instructors/instructor-notes.md" "cae72b6712578d74a49fea7513099f8c" "site/built/instructor-notes.md" "2024-12-03"
-"learners/setup.Rmd" "77fbe8e4496a89da69d9bcae582cac64" "site/built/setup.md" "2024-12-03"
-"old_carpentries_incubator/404.md" "5e864846045fca3e8d82fa69eaefa5f0" "site/built/404.md" "2024-12-03"
-"old_carpentries_incubator/aio.md" "18553f83976668567aa30777afd7c719" "site/built/aio.md" "2024-12-03"
-"old_carpentries_incubator/reference.md" "0e582dab8c7f586fb96bb1dcf1ca6b4c" "site/built/reference.md" "2024-12-03"
-"profiles/learner-profiles.md" "60b93493cf1da06dfd63255d73854461" "site/built/learner-profiles.md" "2024-12-03"
-"renv/profiles/lesson-requirements/renv.lock" "d2267727c0cb4a7ac9628d6bfd1c4cac" "site/built/renv.lock" "2024-12-03"
+"CODE_OF_CONDUCT.md" "06f4c4289ab6bb4db4fa69f818cf24ba" "site/built/CODE_OF_CONDUCT.md" "2024-12-10"
+"LICENSE.md" "8a0a618b3207e1817844a86db497bff9" "site/built/LICENSE.md" "2024-12-10"
+"config.yaml" "75323286755b184e154f3123eb45ef38" "site/built/config.yaml" "2024-12-10"
+"index.md" "000a1a2b1e4e4f274b3dbff311b49818" "site/built/index.md" "2024-12-10"
+"links.md" "8184cf4149eafbf03ce8da8ff0778c14" "site/built/links.md" "2024-12-10"
+"episodes/01-introduction.Rmd" "d32b6b5562a66dc90d79acbf60210375" "site/built/01-introduction.md" "2024-12-10"
+"episodes/02-shell_to_cwl.Rmd" "9d08ba8ae7875dee96e8f80de70907ea" "site/built/02-shell_to_cwl.md" "2024-12-10"
+"episodes/03-dependency_graphs.Rmd" "f55a067639c7f056312d9e137fdf2ed6" "site/built/03-dependency_graphs.md" "2024-12-10"
+"episodes/04-reusing_tools.Rmd" "4a90245e02110dbb13296102d3ce75a2" "site/built/04-reusing_tools.md" "2024-12-10"
+"episodes/addendum-01-debug.Rmd" "3ce548abd8cb1934aa12b16cd62104e3" "site/built/addendum-01-debug.md" "2024-12-10"
+"episodes/more_info.md" "b97f3b7186f568f33352041b7e2449ff" "site/built/more_info.md" "2024-12-10"
+"instructors/instructor-notes.md" "cae72b6712578d74a49fea7513099f8c" "site/built/instructor-notes.md" "2024-12-10"
+"learners/setup.Rmd" "77fbe8e4496a89da69d9bcae582cac64" "site/built/setup.md" "2024-12-10"
+"old_carpentries_incubator/404.md" "5e864846045fca3e8d82fa69eaefa5f0" "site/built/404.md" "2024-12-10"
+"old_carpentries_incubator/aio.md" "18553f83976668567aa30777afd7c719" "site/built/aio.md" "2024-12-10"
+"old_carpentries_incubator/reference.md" "0e582dab8c7f586fb96bb1dcf1ca6b4c" "site/built/reference.md" "2024-12-10"
+"profiles/learner-profiles.md" "60b93493cf1da06dfd63255d73854461" "site/built/learner-profiles.md" "2024-12-10"
+"renv/profiles/lesson-requirements/renv.lock" "d2267727c0cb4a7ac9628d6bfd1c4cac" "site/built/renv.lock" "2024-12-10"
diff --git a/more_info.html b/more_info.html
index 6cc7b3d..9cf6d55 100644
--- a/more_info.html
+++ b/more_info.html
@@ -318,7 +318,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1>More Information</h1>
-        <p>Last updated on 2024-12-03 |
+        <p>Last updated on 2024-12-10 |
 
         <a href="https://github.com/__USERNAME__/__PROJECT__/edit/main/episodes/more_info.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 
@@ -406,8 +406,8 @@ <h1>More Information</h1>
   "url": "https://__USERNAME__.github.io/__PROJECT__/more_info.html",
   "identifier": "https://__USERNAME__.github.io/__PROJECT__/more_info.html",
   "dateCreated": "2024-04-29",
-  "dateModified": "2024-12-03",
-  "datePublished": "2024-12-03"
+  "dateModified": "2024-12-10",
+  "datePublished": "2024-12-10"
 }
 
   </script><script>
diff --git a/pkgdown.yml b/pkgdown.yml
index 33d2d46..fb496c2 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,4 +2,4 @@ pandoc: 3.1.11
 pkgdown: 2.1.1
 pkgdown_sha: ~
 articles: {}
-last_built: 2024-12-03T01:52Z
+last_built: 2024-12-10T00:30Z
diff --git a/profiles.html b/profiles.html
index 9100987..dea5d0b 100644
--- a/profiles.html
+++ b/profiles.html
@@ -351,8 +351,8 @@ <h1>Learner Profiles</h1>
   "url": "https://__USERNAME__.github.io/__PROJECT__/profiles.html",
   "identifier": "https://__USERNAME__.github.io/__PROJECT__/profiles.html",
   "dateCreated": "2024-04-29",
-  "dateModified": "2024-12-03",
-  "datePublished": "2024-12-03"
+  "dateModified": "2024-12-10",
+  "datePublished": "2024-12-10"
 }
 
   </script><script>
diff --git a/reference.html b/reference.html
index dc91137..afa03b4 100644
--- a/reference.html
+++ b/reference.html
@@ -314,7 +314,7 @@ <h2 class="accordion-header" id="flush-headingTwelve">
       </div>
       <hr></nav><main id="main-content" class="main-content"><div class="container lesson-content">
         <h1></h1>
-        <p>Last updated on 2024-12-03 |
+        <p>Last updated on 2024-12-10 |
 
         <a href="https://github.com/__USERNAME__/__PROJECT__/edit/main/old_carpentries_incubator/reference.md" class="external-link">Edit this page <i aria-hidden="true" data-feather="edit"></i></a></p>
 
@@ -390,8 +390,8 @@ <h1></h1>
   "url": "https://__USERNAME__.github.io/__PROJECT__/reference.html",
   "identifier": "https://__USERNAME__.github.io/__PROJECT__/reference.html",
   "dateCreated": "2024-04-29",
-  "dateModified": "2024-12-03",
-  "datePublished": "2024-12-03"
+  "dateModified": "2024-12-10",
+  "datePublished": "2024-12-10"
 }
 
   </script><script>