From badce78404ca168ee554d2006874342e7307a7ce Mon Sep 17 00:00:00 2001
From: GitHub Actions <actions@github.com>
Date: Thu, 9 May 2024 03:27:33 +0000
Subject: [PATCH] site deploy

Auto-generated via {sandpaper}
Source  : efe39bcabd9f60ea5baba56ee941011d29deb370
Branch  : md-outputs
Author  : GitHub Actions <actions@github.com>
Time    : 2024-05-09 03:27:20 +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
---
 03-dependency_graphs.html            | 26 ++++++++--------
 04-reusing_tools.html                | 10 +++---
 addendum-01-debug.html               | 10 +++---
 aio.html                             | 46 +++++++++++++++-------------
 files/data_setup.Rmd                 |  8 +++--
 index.html                           | 24 ++++++++-------
 instructor/03-dependency_graphs.html | 26 ++++++++--------
 instructor/04-reusing_tools.html     | 10 +++---
 instructor/addendum-01-debug.html    | 10 +++---
 instructor/aio.html                  | 46 +++++++++++++++-------------
 instructor/index.html                | 24 ++++++++-------
 md5sum.txt                           |  4 +--
 pkgdown.yml                          |  2 +-
 13 files changed, 130 insertions(+), 116 deletions(-)

diff --git a/03-dependency_graphs.html b/03-dependency_graphs.html
index c6abfe5..a221815 100644
--- a/03-dependency_graphs.html
+++ b/03-dependency_graphs.html
@@ -354,7 +354,7 @@ <h3 class="callout-title">Naming steps<a class="anchor" aria-label="anchor" href
   <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" 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">
 <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>
@@ -503,7 +503,7 @@ <h3 class="callout-title">Is this a valid workflow? 🌶<a class="anchor" aria-l
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb2">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -519,25 +519,27 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 rna_seq_workflow_2.cwl:51:11: Source 'alignment' of type ["File", {"type": "array", "items":
                               "File"}] may be incompatible
 rna_seq_workflow_2.cwl:56:7:    with sink 'bam_sorted' of type "File"</code></pre>
-<div id="whats-in-a-warning" class="callout discussion">
+<p><br></p>
+<div id="should-we-be-concerned-about-this-warning" class="callout discussion">
 <div class="callout-square">
 <i class="callout-icon" data-feather="message-circle"></i>
 </div>
-<div id="whats-in-a-warning" class="callout-inner">
-<h3 class="callout-title">What’s in a warning 🌶🌶🌶<a class="anchor" aria-label="anchor" href="#whats-in-a-warning"></a>
+<div id="should-we-be-concerned-about-this-warning" class="callout-inner">
+<h3 class="callout-title">Should we be concerned about this warning
+🌶🌶🌶<a class="anchor" aria-label="anchor" href="#should-we-be-concerned-about-this-warning"></a>
 </h3>
 <div class="callout-content">
-<p>Should we be concerned about this warning?</p>
-<p>If not, why not?</p>
+<p>Not all warnings are bad.<br>
+Should we be concerned about this warning? If not, why not?</p>
 </div>
 </div>
 </div>
 <div id="accordionSolution2" class="accordion challenge-accordion accordion-flush">
 <div class="accordion-item">
 <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">Not all warnings are bad</h4>
+  <h4 class="accordion-header" id="headingSolution2">Show me the solution</h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <p>In this case, the outputs of the mapping step may instead either be
 just one file, OR an array of files.</p>
@@ -558,7 +560,7 @@ <h4 class="accordion-header" id="headingSolution2">Not all warnings are bad</h4>
   <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" 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">
 <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>
@@ -608,7 +610,7 @@ <h3 class="callout-title">Challenge: Draw the workflow 🌶<a class="anchor" ari
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <p>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>
@@ -688,7 +690,7 @@ <h3 class="callout-title">Push your workflow to GitHub 🌶<a class="anchor" ari
 <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" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <p>Your solution might look like this</p>
 <div class="codewrapper sourceCode" id="cb6">
diff --git a/04-reusing_tools.html b/04-reusing_tools.html
index 571bc2f..527cf21 100644
--- a/04-reusing_tools.html
+++ b/04-reusing_tools.html
@@ -342,7 +342,7 @@ <h3 class="callout-title">Find the featureCounts tool in the
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <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>
@@ -390,7 +390,7 @@ <h3 class="callout-title">Add the featureCounts tool to the workflow
 <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" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
 <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>
@@ -403,7 +403,7 @@ <h4 class="accordion-header" id="headingHint1">Hint: Feature Counts Workflow Ste
 <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" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
 <div class="accordion-body">
 <p>Use a <code>requirements</code> entry with
 <code>ResourceRequirement</code> to allocate a <code>ramMin</code> of
@@ -417,7 +417,7 @@ <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" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <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>
@@ -515,7 +515,7 @@ <h3 class="code-label">YAML<i aria-hidden="true" data-feather="chevron-left"></i
   <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" 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">
 <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>
diff --git a/addendum-01-debug.html b/addendum-01-debug.html
index 1f5ec8d..8c9eebc 100644
--- a/addendum-01-debug.html
+++ b/addendum-01-debug.html
@@ -368,7 +368,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
   <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" 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><code>ERROR Tool definition failed validation:
 while scanning for the next token
@@ -442,7 +442,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
   <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" 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>ERROR Tool definition failed validation:
 rna_seq_workflow_fieldname_fail.cwl:1:1:   Object `rna_seq_workflow_fieldname_fail.cwl` is not valid
@@ -535,7 +535,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
   <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" aria-labelledby="headingSpoiler3" data-bs-parent="#accordionSpoiler3">
+<div id="collapseSpoiler3" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler3" aria-labelledby="headingSpoiler3">
 <div class="accordion-body">
 <pre><code>ERROR Tool definition failed validation:
 rna_seq_workflow_varname_fail.cwl:8:1:  checking field `steps`
@@ -658,7 +658,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
   <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" aria-labelledby="headingSpoiler4" data-bs-parent="#accordionSpoiler4">
+<div id="collapseSpoiler4" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler4" aria-labelledby="headingSpoiler4">
 <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"
@@ -761,7 +761,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
   <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" aria-labelledby="headingSpoiler5" data-bs-parent="#accordionSpoiler5">
+<div id="collapseSpoiler5" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler5" aria-labelledby="headingSpoiler5">
 <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
diff --git a/aio.html b/aio.html
index 0dd459a..775ae62 100644
--- a/aio.html
+++ b/aio.html
@@ -1454,7 +1454,7 @@ <h3 class="callout-title">Naming steps<a class="anchor" aria-label="anchor" href
   <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" 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">
 <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>
@@ -1604,7 +1604,7 @@ <h3 class="callout-title">Is this a valid workflow? 🌶<a class="anchor" aria-l
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb2">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1620,25 +1620,27 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 rna_seq_workflow_2.cwl:51:11: Source 'alignment' of type ["File", {"type": "array", "items":
                               "File"}] may be incompatible
 rna_seq_workflow_2.cwl:56:7:    with sink 'bam_sorted' of type "File"</code></pre>
-<div id="whats-in-a-warning" class="callout discussion">
+<p><br></p>
+<div id="should-we-be-concerned-about-this-warning" class="callout discussion">
 <div class="callout-square">
 <i class="callout-icon" data-feather="message-circle"></i>
 </div>
-<div id="whats-in-a-warning" class="callout-inner">
-<h3 class="callout-title">What’s in a warning 🌶🌶🌶<a class="anchor" aria-label="anchor" href="#whats-in-a-warning"></a>
+<div id="should-we-be-concerned-about-this-warning" class="callout-inner">
+<h3 class="callout-title">Should we be concerned about this warning
+🌶🌶🌶<a class="anchor" aria-label="anchor" href="#should-we-be-concerned-about-this-warning"></a>
 </h3>
 <div class="callout-content">
-<p>Should we be concerned about this warning?</p>
-<p>If not, why not?</p>
+<p>Not all warnings are bad.<br>
+Should we be concerned about this warning? If not, why not?</p>
 </div>
 </div>
 </div>
 <div id="accordionSolution2" class="accordion challenge-accordion accordion-flush">
 <div class="accordion-item">
 <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">Not all warnings are bad</h4>
+  <h4 class="accordion-header" id="headingSolution2">Show me the solution</h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <p>In this case, the outputs of the mapping step may instead either be
 just one file, OR an array of files.</p>
@@ -1660,7 +1662,7 @@ <h4 class="accordion-header" id="headingSolution2">Not all warnings are bad</h4>
   <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" 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">
 <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>
@@ -1711,7 +1713,7 @@ <h3 class="callout-title">Challenge: Draw the workflow 🌶<a class="anchor" ari
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <p>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>
@@ -1796,7 +1798,7 @@ <h3 class="callout-title">Push your workflow to GitHub 🌶<a class="anchor" ari
 <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" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <p>Your solution might look like this</p>
 <div class="codewrapper sourceCode" id="cb6">
@@ -1973,7 +1975,7 @@ <h3 class="callout-title">Find the featureCounts tool in the
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <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>
@@ -2022,7 +2024,7 @@ <h3 class="callout-title">Add the featureCounts tool to the workflow
 <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" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
 <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>
@@ -2035,7 +2037,7 @@ <h4 class="accordion-header" id="headingHint1">Hint: Feature Counts Workflow Ste
 <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" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
 <div class="accordion-body">
 <p>Use a <code>requirements</code> entry with
 <code>ResourceRequirement</code> to allocate a <code>ramMin</code> of
@@ -2049,7 +2051,7 @@ <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" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <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>
@@ -2148,7 +2150,7 @@ <h3 class="code-label">YAML<i aria-hidden="true" data-feather="chevron-left"></i
   <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" 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">
 <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>
@@ -2306,7 +2308,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
   <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" 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><code>ERROR Tool definition failed validation:
 while scanning for the next token
@@ -2381,7 +2383,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
   <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" 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>ERROR Tool definition failed validation:
 rna_seq_workflow_fieldname_fail.cwl:1:1:   Object `rna_seq_workflow_fieldname_fail.cwl` is not valid
@@ -2475,7 +2477,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
   <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" aria-labelledby="headingSpoiler3" data-bs-parent="#accordionSpoiler3">
+<div id="collapseSpoiler3" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler3" aria-labelledby="headingSpoiler3">
 <div class="accordion-body">
 <pre><code>ERROR Tool definition failed validation:
 rna_seq_workflow_varname_fail.cwl:8:1:  checking field `steps`
@@ -2600,7 +2602,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
   <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" aria-labelledby="headingSpoiler4" data-bs-parent="#accordionSpoiler4">
+<div id="collapseSpoiler4" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler4" aria-labelledby="headingSpoiler4">
 <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"
@@ -2704,7 +2706,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
   <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" aria-labelledby="headingSpoiler5" data-bs-parent="#accordionSpoiler5">
+<div id="collapseSpoiler5" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler5" aria-labelledby="headingSpoiler5">
 <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
diff --git a/files/data_setup.Rmd b/files/data_setup.Rmd
index cf67761..479d332 100644
--- a/files/data_setup.Rmd
+++ b/files/data_setup.Rmd
@@ -78,13 +78,15 @@ We should exclude the rnaseq folder from being tracked in this repository.
 echo 'rnaseq/' >> .gitignore
 ```
 
-### Add .gitignore to git
+### Add our changes to git
 
 `.gitignore` is a file that is tracked like all other GitHub commands.  
 
+Likewise, we also need to let git know we would like to keep bio-cwl-tools as a submodule.  
+
 ```
-git add .gitignore
-git commit -m "Don't track files in the rnaseq directory"
+git add .gitignore bio-cwl-tools
+git commit -m "Don't track files in rnaseq dir, added bio-cwl-tools as a submodule"
 git push
 ```
 
diff --git a/index.html b/index.html
index f22ae46..a5e83fd 100644
--- a/index.html
+++ b/index.html
@@ -701,7 +701,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
   <h3 class="accordion-header" id="headingSpoiler1">
 <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>Docker Version Output Example</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>Client: Docker Engine - Community
  Version:           20.10.13
@@ -752,7 +752,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
   <h3 class="accordion-header" id="headingSpoiler2">
 <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>Cwltool Version Output Example</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>/home/learner/env/bin/cwltool 3.1.20220224085855</code></pre>
 </div>
@@ -776,7 +776,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
   <h3 class="accordion-header" id="headingSpoiler3">
 <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>Graphviz version output example</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>dot - graphviz version 2.43.0 (0)</code></pre>
 </div>
@@ -935,11 +935,13 @@ <h3 id="ignore-data-files-in-git">Ignore data files in Git<a class="anchor" aria
 <pre><code>echo 'rnaseq/' &gt;&gt; .gitignore</code></pre>
 </div>
 <div class="section level3">
-<h3 id="add--gitignore-to-git">Add .gitignore to git<a class="anchor" aria-label="anchor" href="#add--gitignore-to-git"></a></h3>
+<h3 id="add-our-changes-to-git">Add our changes to git<a class="anchor" aria-label="anchor" href="#add-our-changes-to-git"></a></h3>
 <p><code>.gitignore</code> is a file that is tracked like all other
 GitHub commands.</p>
-<pre><code>git add .gitignore
-git commit -m "Don't track files in the rnaseq directory"
+<p>Likewise, we also need to let git know we would like to keep
+bio-cwl-tools as a submodule.</p>
+<pre><code>git add .gitignore bio-cwl-tools
+git commit -m "Don't track files in rnaseq dir, added bio-cwl-tools as a submodule"
 git push</code></pre>
 <p><br></p>
 </div>
@@ -956,7 +958,7 @@ <h3 id="star-genome-index">STAR Genome index<a class="anchor" aria-label="anchor
   <h3 class="accordion-header" id="headingSpoiler4">
 <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>Option 1: Download the index</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">
 <p>At least 9 GB of memory is required to generate the index, which will
 occupy 3.3GB of disk.</p>
@@ -979,7 +981,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
   <h3 class="accordion-header" id="headingSpoiler5">
 <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>Option 2: Generate the index yourself</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">
 <p>To generate the genome index yourself: create a new file named
 <code>dm6-star-index.yaml</code> in the the
@@ -1060,7 +1062,7 @@ <h4 id="setting-the-checksum-">Setting the checksum.<a class="anchor" aria-label
   <h3 class="accordion-header" id="headingSpoiler6">
 <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>rnaseq.md5</h3>
 </button>
-<div id="collapseSpoiler6" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler6" aria-labelledby="headingSpoiler6">
+<div id="collapseSpoiler6" class="accordion-collapse collapse" aria-labelledby="headingSpoiler6" data-bs-parent="#accordionSpoiler6">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb38">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1096,7 +1098,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
   <h3 class="accordion-header" id="headingSpoiler7">
 <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>make_md5.sh</h3>
 </button>
-<div id="collapseSpoiler7" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler7" aria-labelledby="headingSpoiler7">
+<div id="collapseSpoiler7" class="accordion-collapse collapse" aria-labelledby="headingSpoiler7" data-bs-parent="#accordionSpoiler7">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb39">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1142,7 +1144,7 @@ <h4 id="checking-your-files">Checking your files<a class="anchor" aria-label="an
   <h3 class="accordion-header" id="headingSpoiler8">
 <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>md5sum check command outputs</h3>
 </button>
-<div id="collapseSpoiler8" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler8" aria-labelledby="headingSpoiler8">
+<div id="collapseSpoiler8" class="accordion-collapse collapse" aria-labelledby="headingSpoiler8" data-bs-parent="#accordionSpoiler8">
 <div class="accordion-body">
 <p>We expect the following outputs from this command:</p>
 <pre><code><span><span class="va">Drosophila_melanogaster.BDGP6.87.gtf</span><span class="op">:</span> <span class="va">OK</span></span>
diff --git a/instructor/03-dependency_graphs.html b/instructor/03-dependency_graphs.html
index 08c76ce..3ff8b8e 100644
--- a/instructor/03-dependency_graphs.html
+++ b/instructor/03-dependency_graphs.html
@@ -355,7 +355,7 @@ <h3 class="callout-title">Naming steps<a class="anchor" aria-label="anchor" href
   <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" 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">
 <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>
@@ -504,7 +504,7 @@ <h3 class="callout-title">Is this a valid workflow? 🌶<a class="anchor" aria-l
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb2">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -520,25 +520,27 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 rna_seq_workflow_2.cwl:51:11: Source 'alignment' of type ["File", {"type": "array", "items":
                               "File"}] may be incompatible
 rna_seq_workflow_2.cwl:56:7:    with sink 'bam_sorted' of type "File"</code></pre>
-<div id="whats-in-a-warning" class="callout discussion">
+<p><br></p>
+<div id="should-we-be-concerned-about-this-warning" class="callout discussion">
 <div class="callout-square">
 <i class="callout-icon" data-feather="message-circle"></i>
 </div>
-<div id="whats-in-a-warning" class="callout-inner">
-<h3 class="callout-title">What’s in a warning 🌶🌶🌶<a class="anchor" aria-label="anchor" href="#whats-in-a-warning"></a>
+<div id="should-we-be-concerned-about-this-warning" class="callout-inner">
+<h3 class="callout-title">Should we be concerned about this warning
+🌶🌶🌶<a class="anchor" aria-label="anchor" href="#should-we-be-concerned-about-this-warning"></a>
 </h3>
 <div class="callout-content">
-<p>Should we be concerned about this warning?</p>
-<p>If not, why not?</p>
+<p>Not all warnings are bad.<br>
+Should we be concerned about this warning? If not, why not?</p>
 </div>
 </div>
 </div>
 <div id="accordionSolution2" class="accordion challenge-accordion accordion-flush">
 <div class="accordion-item">
 <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">Not all warnings are bad</h4>
+  <h4 class="accordion-header" id="headingSolution2">Show me the solution</h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <p>In this case, the outputs of the mapping step may instead either be
 just one file, OR an array of files.</p>
@@ -559,7 +561,7 @@ <h4 class="accordion-header" id="headingSolution2">Not all warnings are bad</h4>
   <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" 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">
 <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>
@@ -609,7 +611,7 @@ <h3 class="callout-title">Challenge: Draw the workflow 🌶<a class="anchor" ari
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <p>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>
@@ -689,7 +691,7 @@ <h3 class="callout-title">Push your workflow to GitHub 🌶<a class="anchor" ari
 <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" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <p>Your solution might look like this</p>
 <div class="codewrapper sourceCode" id="cb6">
diff --git a/instructor/04-reusing_tools.html b/instructor/04-reusing_tools.html
index 17c8901..4aa945b 100644
--- a/instructor/04-reusing_tools.html
+++ b/instructor/04-reusing_tools.html
@@ -343,7 +343,7 @@ <h3 class="callout-title">Find the featureCounts tool in the
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <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>
@@ -391,7 +391,7 @@ <h3 class="callout-title">Add the featureCounts tool to the workflow
 <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" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
 <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>
@@ -404,7 +404,7 @@ <h4 class="accordion-header" id="headingHint1">Hint: Feature Counts Workflow Ste
 <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" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
 <div class="accordion-body">
 <p>Use a <code>requirements</code> entry with
 <code>ResourceRequirement</code> to allocate a <code>ramMin</code> of
@@ -418,7 +418,7 @@ <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" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <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>
@@ -516,7 +516,7 @@ <h3 class="code-label">YAML<i aria-hidden="true" data-feather="chevron-left"></i
   <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" 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">
 <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>
diff --git a/instructor/addendum-01-debug.html b/instructor/addendum-01-debug.html
index d798536..1186a0c 100644
--- a/instructor/addendum-01-debug.html
+++ b/instructor/addendum-01-debug.html
@@ -369,7 +369,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
   <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" 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><code>ERROR Tool definition failed validation:
 while scanning for the next token
@@ -443,7 +443,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
   <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" 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>ERROR Tool definition failed validation:
 rna_seq_workflow_fieldname_fail.cwl:1:1:   Object `rna_seq_workflow_fieldname_fail.cwl` is not valid
@@ -536,7 +536,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
   <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" aria-labelledby="headingSpoiler3" data-bs-parent="#accordionSpoiler3">
+<div id="collapseSpoiler3" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler3" aria-labelledby="headingSpoiler3">
 <div class="accordion-body">
 <pre><code>ERROR Tool definition failed validation:
 rna_seq_workflow_varname_fail.cwl:8:1:  checking field `steps`
@@ -659,7 +659,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
   <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" aria-labelledby="headingSpoiler4" data-bs-parent="#accordionSpoiler4">
+<div id="collapseSpoiler4" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler4" aria-labelledby="headingSpoiler4">
 <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"
@@ -762,7 +762,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
   <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" aria-labelledby="headingSpoiler5" data-bs-parent="#accordionSpoiler5">
+<div id="collapseSpoiler5" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler5" aria-labelledby="headingSpoiler5">
 <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
diff --git a/instructor/aio.html b/instructor/aio.html
index dc41ea2..d97bddc 100644
--- a/instructor/aio.html
+++ b/instructor/aio.html
@@ -1474,7 +1474,7 @@ <h3 class="callout-title">Naming steps<a class="anchor" aria-label="anchor" href
   <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" 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">
 <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>
@@ -1624,7 +1624,7 @@ <h3 class="callout-title">Is this a valid workflow? 🌶<a class="anchor" aria-l
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb2">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1640,25 +1640,27 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 rna_seq_workflow_2.cwl:51:11: Source 'alignment' of type ["File", {"type": "array", "items":
                               "File"}] may be incompatible
 rna_seq_workflow_2.cwl:56:7:    with sink 'bam_sorted' of type "File"</code></pre>
-<div id="whats-in-a-warning" class="callout discussion">
+<p><br></p>
+<div id="should-we-be-concerned-about-this-warning" class="callout discussion">
 <div class="callout-square">
 <i class="callout-icon" data-feather="message-circle"></i>
 </div>
-<div id="whats-in-a-warning" class="callout-inner">
-<h3 class="callout-title">What’s in a warning 🌶🌶🌶<a class="anchor" aria-label="anchor" href="#whats-in-a-warning"></a>
+<div id="should-we-be-concerned-about-this-warning" class="callout-inner">
+<h3 class="callout-title">Should we be concerned about this warning
+🌶🌶🌶<a class="anchor" aria-label="anchor" href="#should-we-be-concerned-about-this-warning"></a>
 </h3>
 <div class="callout-content">
-<p>Should we be concerned about this warning?</p>
-<p>If not, why not?</p>
+<p>Not all warnings are bad.<br>
+Should we be concerned about this warning? If not, why not?</p>
 </div>
 </div>
 </div>
 <div id="accordionSolution2" class="accordion challenge-accordion accordion-flush">
 <div class="accordion-item">
 <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">Not all warnings are bad</h4>
+  <h4 class="accordion-header" id="headingSolution2">Show me the solution</h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <p>In this case, the outputs of the mapping step may instead either be
 just one file, OR an array of files.</p>
@@ -1680,7 +1682,7 @@ <h4 class="accordion-header" id="headingSolution2">Not all warnings are bad</h4>
   <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" 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">
 <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>
@@ -1731,7 +1733,7 @@ <h3 class="callout-title">Challenge: Draw the workflow 🌶<a class="anchor" ari
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3">Show me the solution</h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" data-bs-parent="#accordionSolution3" aria-labelledby="headingSolution3">
+<div id="collapseSolution3" class="accordion-collapse collapse" aria-labelledby="headingSolution3" data-bs-parent="#accordionSolution3">
 <div class="accordion-body">
 <p>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>
@@ -1816,7 +1818,7 @@ <h3 class="callout-title">Push your workflow to GitHub 🌶<a class="anchor" ari
 <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" data-bs-parent="#accordionSolution4" aria-labelledby="headingSolution4">
+<div id="collapseSolution4" class="accordion-collapse collapse" aria-labelledby="headingSolution4" data-bs-parent="#accordionSolution4">
 <div class="accordion-body">
 <p>Your solution might look like this</p>
 <div class="codewrapper sourceCode" id="cb6">
@@ -1994,7 +1996,7 @@ <h3 class="callout-title">Find the featureCounts tool in the
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1">Show me the solution</h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
 <div class="accordion-body">
 <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>
@@ -2043,7 +2045,7 @@ <h3 class="callout-title">Add the featureCounts tool to the workflow
 <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" data-bs-parent="#accordionHint1" aria-labelledby="headingHint1">
+<div id="collapseHint1" class="accordion-collapse collapse" aria-labelledby="headingHint1" data-bs-parent="#accordionHint1">
 <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>
@@ -2056,7 +2058,7 @@ <h4 class="accordion-header" id="headingHint1">Hint: Feature Counts Workflow Ste
 <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" data-bs-parent="#accordionHint2" aria-labelledby="headingHint2">
+<div id="collapseHint2" class="accordion-collapse collapse" aria-labelledby="headingHint2" data-bs-parent="#accordionHint2">
 <div class="accordion-body">
 <p>Use a <code>requirements</code> entry with
 <code>ResourceRequirement</code> to allocate a <code>ramMin</code> of
@@ -2070,7 +2072,7 @@ <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" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <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>
@@ -2169,7 +2171,7 @@ <h3 class="code-label">YAML<i aria-hidden="true" data-feather="chevron-left"></i
   <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" 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">
 <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>
@@ -2328,7 +2330,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
   <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" 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><code>ERROR Tool definition failed validation:
 while scanning for the next token
@@ -2403,7 +2405,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
   <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" 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>ERROR Tool definition failed validation:
 rna_seq_workflow_fieldname_fail.cwl:1:1:   Object `rna_seq_workflow_fieldname_fail.cwl` is not valid
@@ -2497,7 +2499,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
   <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" aria-labelledby="headingSpoiler3" data-bs-parent="#accordionSpoiler3">
+<div id="collapseSpoiler3" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler3" aria-labelledby="headingSpoiler3">
 <div class="accordion-body">
 <pre><code>ERROR Tool definition failed validation:
 rna_seq_workflow_varname_fail.cwl:8:1:  checking field `steps`
@@ -2622,7 +2624,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
   <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" aria-labelledby="headingSpoiler4" data-bs-parent="#accordionSpoiler4">
+<div id="collapseSpoiler4" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler4" aria-labelledby="headingSpoiler4">
 <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"
@@ -2726,7 +2728,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
   <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" aria-labelledby="headingSpoiler5" data-bs-parent="#accordionSpoiler5">
+<div id="collapseSpoiler5" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler5" aria-labelledby="headingSpoiler5">
 <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
diff --git a/instructor/index.html b/instructor/index.html
index a9fb9f3..b272424 100644
--- a/instructor/index.html
+++ b/instructor/index.html
@@ -765,7 +765,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
   <h3 class="accordion-header" id="headingSpoiler1">
 <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>Docker Version Output Example</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>Client: Docker Engine - Community
  Version:           20.10.13
@@ -816,7 +816,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
   <h3 class="accordion-header" id="headingSpoiler2">
 <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>Cwltool Version Output Example</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>/home/learner/env/bin/cwltool 3.1.20220224085855</code></pre>
 </div>
@@ -840,7 +840,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
   <h3 class="accordion-header" id="headingSpoiler3">
 <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>Graphviz version output example</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>dot - graphviz version 2.43.0 (0)</code></pre>
 </div>
@@ -999,11 +999,13 @@ <h3 id="ignore-data-files-in-git">Ignore data files in Git<a class="anchor" aria
 <pre><code>echo 'rnaseq/' &gt;&gt; .gitignore</code></pre>
 </div>
 <div class="section level3">
-<h3 id="add--gitignore-to-git">Add .gitignore to git<a class="anchor" aria-label="anchor" href="#add--gitignore-to-git"></a></h3>
+<h3 id="add-our-changes-to-git">Add our changes to git<a class="anchor" aria-label="anchor" href="#add-our-changes-to-git"></a></h3>
 <p><code>.gitignore</code> is a file that is tracked like all other
 GitHub commands.</p>
-<pre><code>git add .gitignore
-git commit -m "Don't track files in the rnaseq directory"
+<p>Likewise, we also need to let git know we would like to keep
+bio-cwl-tools as a submodule.</p>
+<pre><code>git add .gitignore bio-cwl-tools
+git commit -m "Don't track files in rnaseq dir, added bio-cwl-tools as a submodule"
 git push</code></pre>
 <p><br></p>
 </div>
@@ -1020,7 +1022,7 @@ <h3 id="star-genome-index">STAR Genome index<a class="anchor" aria-label="anchor
   <h3 class="accordion-header" id="headingSpoiler4">
 <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>Option 1: Download the index</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">
 <p>At least 9 GB of memory is required to generate the index, which will
 occupy 3.3GB of disk.</p>
@@ -1043,7 +1045,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
   <h3 class="accordion-header" id="headingSpoiler5">
 <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>Option 2: Generate the index yourself</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">
 <p>To generate the genome index yourself: create a new file named
 <code>dm6-star-index.yaml</code> in the the
@@ -1124,7 +1126,7 @@ <h4 id="setting-the-checksum-">Setting the checksum.<a class="anchor" aria-label
   <h3 class="accordion-header" id="headingSpoiler6">
 <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>rnaseq.md5</h3>
 </button>
-<div id="collapseSpoiler6" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler6" aria-labelledby="headingSpoiler6">
+<div id="collapseSpoiler6" class="accordion-collapse collapse" aria-labelledby="headingSpoiler6" data-bs-parent="#accordionSpoiler6">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb38">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1160,7 +1162,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
   <h3 class="accordion-header" id="headingSpoiler7">
 <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>make_md5.sh</h3>
 </button>
-<div id="collapseSpoiler7" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler7" aria-labelledby="headingSpoiler7">
+<div id="collapseSpoiler7" class="accordion-collapse collapse" aria-labelledby="headingSpoiler7" data-bs-parent="#accordionSpoiler7">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb39">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1206,7 +1208,7 @@ <h4 id="checking-your-files">Checking your files<a class="anchor" aria-label="an
   <h3 class="accordion-header" id="headingSpoiler8">
 <div class="note-square"><i aria-hidden="true" class="callout-icon" data-feather="eye"></i></div>md5sum check command outputs</h3>
 </button>
-<div id="collapseSpoiler8" class="accordion-collapse collapse" data-bs-parent="#accordionSpoiler8" aria-labelledby="headingSpoiler8">
+<div id="collapseSpoiler8" class="accordion-collapse collapse" aria-labelledby="headingSpoiler8" data-bs-parent="#accordionSpoiler8">
 <div class="accordion-body">
 <p>We expect the following outputs from this command:</p>
 <pre><code><span><span class="va">Drosophila_melanogaster.BDGP6.87.gtf</span><span class="op">:</span> <span class="va">OK</span></span>
diff --git a/md5sum.txt b/md5sum.txt
index e901ee0..cc1cf8e 100644
--- a/md5sum.txt
+++ b/md5sum.txt
@@ -6,12 +6,12 @@
 "links.md" "8184cf4149eafbf03ce8da8ff0778c14" "site/built/links.md" "2024-05-09"
 "episodes/01-introduction.Rmd" "d32b6b5562a66dc90d79acbf60210375" "site/built/01-introduction.md" "2024-05-09"
 "episodes/02-shell_to_cwl.Rmd" "9d08ba8ae7875dee96e8f80de70907ea" "site/built/02-shell_to_cwl.md" "2024-05-09"
-"episodes/03-dependency_graphs.Rmd" "e992b9ccbd2fb1d8a1a5f6e1d4b2fc18" "site/built/03-dependency_graphs.md" "2024-05-09"
+"episodes/03-dependency_graphs.Rmd" "f55a067639c7f056312d9e137fdf2ed6" "site/built/03-dependency_graphs.md" "2024-05-09"
 "episodes/04-reusing_tools.Rmd" "4a90245e02110dbb13296102d3ce75a2" "site/built/04-reusing_tools.md" "2024-05-09"
 "episodes/addendum-01-debug.Rmd" "3ce548abd8cb1934aa12b16cd62104e3" "site/built/addendum-01-debug.md" "2024-05-09"
 "episodes/more_info.md" "b97f3b7186f568f33352041b7e2449ff" "site/built/more_info.md" "2024-05-09"
 "instructors/instructor-notes.md" "cae72b6712578d74a49fea7513099f8c" "site/built/instructor-notes.md" "2024-05-09"
-"learners/setup.Rmd" "6020a6e393ac568a958d4a536d063984" "site/built/setup.md" "2024-05-09"
+"learners/setup.Rmd" "77fbe8e4496a89da69d9bcae582cac64" "site/built/setup.md" "2024-05-09"
 "old_carpentries_incubator/404.md" "5e864846045fca3e8d82fa69eaefa5f0" "site/built/404.md" "2024-05-09"
 "old_carpentries_incubator/aio.md" "18553f83976668567aa30777afd7c719" "site/built/aio.md" "2024-05-09"
 "old_carpentries_incubator/reference.md" "0e582dab8c7f586fb96bb1dcf1ca6b4c" "site/built/reference.md" "2024-05-09"
diff --git a/pkgdown.yml b/pkgdown.yml
index 2cb61ce..29e87ee 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,5 +2,5 @@ pandoc: 3.1.11
 pkgdown: 2.0.9
 pkgdown_sha: ~
 articles: {}
-last_built: 2024-05-09T02:39Z
+last_built: 2024-05-09T03:27Z