diff --git a/01-getting-started-with-nextflow.html b/01-getting-started-with-nextflow.html
index 7c26970f..dc3c83b6 100644
--- a/01-getting-started-with-nextflow.html
+++ b/01-getting-started-with-nextflow.html
@@ -667,7 +667,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>You should see output similar to the text shown below:</p>
 <div class="codewrapper">
diff --git a/03-channels.html b/03-channels.html
index c9361f32..5a77b71a 100644
--- a/03-channels.html
+++ b/03-channels.html
@@ -488,7 +488,7 @@ <h3 class="callout-title">Queue vs Value Channel.<a class="anchor" aria-label="a
 <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">
 <ol style="list-style-type: decimal"><li>A queue channels is used to store multiple values.</li>
 <li>A value channel is used to store a single value, this can be a list
@@ -658,7 +658,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb10">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -746,7 +746,7 @@ <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"><
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" 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">
 <div class="codewrapper sourceCode" id="cb15">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -924,7 +924,7 @@ <h3 class="callout-title">Using Channel.fromPath<a class="anchor" aria-label="an
 <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" 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">
 <div class="codewrapper sourceCode" id="cb25">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1093,7 +1093,7 @@ <h3 class="callout-title">Create a channel containing groups of files<a class="a
 <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" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb31">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1114,66 +1114,6 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 </div>
 </div>
-</div>
-<div class="section level3">
-<h3 id="the-fromsra-channel-factory">The <strong>fromSRA</strong> Channel factory<a class="anchor" aria-label="anchor" href="#the-fromsra-channel-factory"></a></h3>
-<p>Another useful factory method is <code>fromSRA</code>. The
-<code>fromSRA</code> method makes it possible to query the <a href="https://www.ncbi.nlm.nih.gov/sra" class="external-link">NCBI SRA</a> archive and returns
-a queue channel emitting the FASTQ files matching the specified
-selection criteria.</p>
-<p>The queries can be project IDs or accession numbers supported by the
-<a href="https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ESearch" class="external-link">NCBI
-ESearch API</a>.</p>
-<p>If you want to use this functionality, you will need an <a href="https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/" class="external-link">NCBI
-API KEY</a>, and to set the environment variable
-<code>NCBI_API_KEY</code> to its value.</p>
-<div class="codewrapper sourceCode" id="cb33">
-<h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="sourceCode groovy" tabindex="0"><code class="sourceCode groovy"><span id="cb33-1"><a href="#cb33-1" tabindex="-1"></a>sra_ch <span class="op">=</span><span class="bu">Channel</span><span class="op">.</span><span class="fu">fromSRA</span><span class="op">(</span><span class="st">'SRP043510'</span><span class="op">)</span></span>
-<span id="cb33-2"><a href="#cb33-2" tabindex="-1"></a>sra_ch<span class="op">.</span><span class="fu">view</span><span class="op">()</span></span></code></pre>
-</div>
-<p>This will print a tuple for every fastq file associated with that SRA
-project accession.</p>
-<div class="codewrapper">
-<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="output" tabindex="0"><code>[SRR1448794, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR144/004/SRR1448794/SRR1448794.fastq.gz]
-[SRR1448795, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR144/005/SRR1448795/SRR1448795.fastq.gz]
-[SRR1448792, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR144/002/SRR1448792/SRR1448792.fastq.gz]
-[SRR1448793, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR144/003/SRR1448793/SRR1448793.fastq.gz]
-[SRR1910483, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR191/003/SRR1910483/SRR1910483.fastq.gz]
-[SRR1910482, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR191/002/SRR1910482/SRR1910482.fastq.gz]
-(remaining omitted)</code></pre>
-</div>
-<p>Multiple accession IDs can be specified using a list object:</p>
-<div class="codewrapper sourceCode" id="cb35">
-<h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="sourceCode groovy" tabindex="0"><code class="sourceCode groovy"><span id="cb35-1"><a href="#cb35-1" tabindex="-1"></a>ids <span class="op">=</span> <span class="op">[</span><span class="st">'ERR908507'</span><span class="op">,</span> <span class="st">'ERR908506'</span><span class="op">,</span> <span class="st">'ERR908505'</span><span class="op">]</span></span>
-<span id="cb35-2"><a href="#cb35-2" tabindex="-1"></a>sra_ch <span class="op">=</span> <span class="bu">Channel</span><span class="op">.</span><span class="fu">fromSRA</span><span class="op">(</span>ids<span class="op">)</span></span>
-<span id="cb35-3"><a href="#cb35-3" tabindex="-1"></a>sra_ch<span class="op">.</span><span class="fu">view</span><span class="op">()</span></span></code></pre>
-</div>
-<div class="codewrapper">
-<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="output" tabindex="0"><code>[ERR908507, [ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908507/ERR908507_1.fastq.gz, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908507/ERR908507_2.fastq.gz]]
-[ERR908506, [ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908506/ERR908506_1.fastq.gz, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908506/ERR908506_2.fastq.gz]]
-[ERR908505, [ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908505/ERR908505_1.fastq.gz, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908505/ERR908505_2.fastq.gz]]</code></pre>
-</div>
-<div id="read-pairs-from-sra" class="callout">
-<div class="callout-square">
-<i class="callout-icon" data-feather="bell"></i>
-</div>
-<div id="read-pairs-from-sra" class="callout-inner">
-<h3 class="callout-title">Read pairs from SRA<a class="anchor" aria-label="anchor" href="#read-pairs-from-sra"></a>
-</h3>
-<div class="callout-content">
-<p>Read pairs are implicitly managed, and are returned as a list of
-files.</p>
-</div>
-</div>
-</div>
 <div id="keypoints1" class="callout keypoints">
 <div class="callout-square">
 <i class="callout-icon" data-feather="key"></i>
diff --git a/12-nfcore.html b/12-nfcore.html
index d5c6b275..ac4095ab 100644
--- a/12-nfcore.html
+++ b/12-nfcore.html
@@ -677,7 +677,7 @@ <h3 class="callout-title">Exercise: listing nf-core pipelines<a class="anchor" a
 <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>Use the <code>--help</code> flag to print the list command usage.</p>
 <div class="codewrapper sourceCode" id="cb9">
@@ -801,7 +801,7 @@ <h3 class="callout-title">Exercise: Fetch the latest RNA-Seq pipeline<a class="a
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <p>Use the <code>nextflow pull</code> command to download the latest
 <code>nf-core/rnaseq</code> pipeline</p>
@@ -911,7 +911,7 @@ <h3 class="callout-title">Exercise : Create nf-core params file<a class="anchor"
 <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">
 <div class="codewrapper sourceCode" id="cb21">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1034,7 +1034,7 @@ <h3 class="callout-title">Exercise create a custom config<a class="anchor" aria-
 <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" 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>A line similar to one below in the file custom.config</p>
 <pre><code><span><span class="va">params.email</span> <span class="op">=</span> <span class="st">"myemail@address.com"</span></span></code></pre>
@@ -1156,7 +1156,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#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" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
 <div class="accordion-body">
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
diff --git a/aio.html b/aio.html
index 874ef1f4..785a0812 100644
--- a/aio.html
+++ b/aio.html
@@ -740,7 +740,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>You should see output similar to the text shown below:</p>
 <div class="codewrapper">
@@ -1303,7 +1303,7 @@ <h3 class="callout-title">Queue vs Value Channel.<a class="anchor" aria-label="a
 <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">
 <ol style="list-style-type: decimal">
 <li>A queue channels is used to store multiple values.</li>
@@ -1489,7 +1489,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb10">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1578,7 +1578,7 @@ <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"><
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" 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">
 <div class="codewrapper sourceCode" id="cb15">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1785,7 +1785,7 @@ <h3 class="callout-title">Using Channel.fromPath<a class="anchor" aria-label="an
 <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" 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">
 <div class="codewrapper sourceCode" id="cb25">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1991,7 +1991,7 @@ <h3 class="callout-title">Create a channel containing groups of files<a class="a
 <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" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb31">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -2012,67 +2012,6 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 </div>
 </div>
-</div>
-<div class="section level3">
-<h3 id="the-fromsra-channel-factory">The <strong>fromSRA</strong> Channel factory<a class="anchor" aria-label="anchor" href="#the-fromsra-channel-factory"></a>
-</h3>
-<p>Another useful factory method is <code>fromSRA</code>. The
-<code>fromSRA</code> method makes it possible to query the <a href="https://www.ncbi.nlm.nih.gov/sra" class="external-link">NCBI SRA</a> archive and returns
-a queue channel emitting the FASTQ files matching the specified
-selection criteria.</p>
-<p>The queries can be project IDs or accession numbers supported by the
-<a href="https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ESearch" class="external-link">NCBI
-ESearch API</a>.</p>
-<p>If you want to use this functionality, you will need an <a href="https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/" class="external-link">NCBI
-API KEY</a>, and to set the environment variable
-<code>NCBI_API_KEY</code> to its value.</p>
-<div class="codewrapper sourceCode" id="cb33">
-<h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="sourceCode groovy" tabindex="0"><code class="sourceCode groovy"><span id="cb33-1"><a href="#cb33-1" tabindex="-1"></a>sra_ch <span class="op">=</span><span class="bu">Channel</span><span class="op">.</span><span class="fu">fromSRA</span><span class="op">(</span><span class="st">'SRP043510'</span><span class="op">)</span></span>
-<span id="cb33-2"><a href="#cb33-2" tabindex="-1"></a>sra_ch<span class="op">.</span><span class="fu">view</span><span class="op">()</span></span></code></pre>
-</div>
-<p>This will print a tuple for every fastq file associated with that SRA
-project accession.</p>
-<div class="codewrapper">
-<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="output" tabindex="0"><code>[SRR1448794, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR144/004/SRR1448794/SRR1448794.fastq.gz]
-[SRR1448795, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR144/005/SRR1448795/SRR1448795.fastq.gz]
-[SRR1448792, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR144/002/SRR1448792/SRR1448792.fastq.gz]
-[SRR1448793, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR144/003/SRR1448793/SRR1448793.fastq.gz]
-[SRR1910483, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR191/003/SRR1910483/SRR1910483.fastq.gz]
-[SRR1910482, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR191/002/SRR1910482/SRR1910482.fastq.gz]
-(remaining omitted)</code></pre>
-</div>
-<p>Multiple accession IDs can be specified using a list object:</p>
-<div class="codewrapper sourceCode" id="cb35">
-<h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="sourceCode groovy" tabindex="0"><code class="sourceCode groovy"><span id="cb35-1"><a href="#cb35-1" tabindex="-1"></a>ids <span class="op">=</span> <span class="op">[</span><span class="st">'ERR908507'</span><span class="op">,</span> <span class="st">'ERR908506'</span><span class="op">,</span> <span class="st">'ERR908505'</span><span class="op">]</span></span>
-<span id="cb35-2"><a href="#cb35-2" tabindex="-1"></a>sra_ch <span class="op">=</span> <span class="bu">Channel</span><span class="op">.</span><span class="fu">fromSRA</span><span class="op">(</span>ids<span class="op">)</span></span>
-<span id="cb35-3"><a href="#cb35-3" tabindex="-1"></a>sra_ch<span class="op">.</span><span class="fu">view</span><span class="op">()</span></span></code></pre>
-</div>
-<div class="codewrapper">
-<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="output" tabindex="0"><code>[ERR908507, [ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908507/ERR908507_1.fastq.gz, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908507/ERR908507_2.fastq.gz]]
-[ERR908506, [ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908506/ERR908506_1.fastq.gz, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908506/ERR908506_2.fastq.gz]]
-[ERR908505, [ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908505/ERR908505_1.fastq.gz, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908505/ERR908505_2.fastq.gz]]</code></pre>
-</div>
-<div id="read-pairs-from-sra" class="callout">
-<div class="callout-square">
-<i class="callout-icon" data-feather="bell"></i>
-</div>
-<div id="read-pairs-from-sra" class="callout-inner">
-<h3 class="callout-title">Read pairs from SRA<a class="anchor" aria-label="anchor" href="#read-pairs-from-sra"></a>
-</h3>
-<div class="callout-content">
-<p>Read pairs are implicitly managed, and are returned as a list of
-files.</p>
-</div>
-</div>
-</div>
 <div id="keypoints1" class="callout keypoints">
 <div class="callout-square">
 <i class="callout-icon" data-feather="key"></i>
@@ -9513,7 +9452,7 @@ <h3 class="callout-title">Exercise: listing nf-core pipelines<a class="anchor" a
 <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>Use the <code>--help</code> flag to print the list command usage.</p>
 <div class="codewrapper sourceCode" id="cb9">
@@ -9642,7 +9581,7 @@ <h3 class="callout-title">Exercise: Fetch the latest RNA-Seq pipeline<a class="a
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <p>Use the <code>nextflow pull</code> command to download the latest
 <code>nf-core/rnaseq</code> pipeline</p>
@@ -9757,7 +9696,7 @@ <h3 class="callout-title">Exercise : Create nf-core params file<a class="anchor"
 <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">
 <div class="codewrapper sourceCode" id="cb21">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -9896,7 +9835,7 @@ <h3 class="callout-title">Exercise create a custom config<a class="anchor" aria-
 <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" 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>A line similar to one below in the file custom.config</p>
 <pre><code><span><span class="va">params.email</span> <span class="op">=</span> <span class="st">"myemail@address.com"</span></span></code></pre>
@@ -10021,7 +9960,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#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" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
 <div class="accordion-body">
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
diff --git a/data/environment.yml b/data/environment.yml
index 4ef8ef47..679a457a 100644
--- a/data/environment.yml
+++ b/data/environment.yml
@@ -3,8 +3,9 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - nextflow=20.10.0
+  - nextflow
   - salmon=1.5
   - fastqc=0.11
-  - multiqc=1.10
+  - multiqc
   - nf-core
+  - graphviz
diff --git a/instructor/01-getting-started-with-nextflow.html b/instructor/01-getting-started-with-nextflow.html
index f01520a2..be5897d8 100644
--- a/instructor/01-getting-started-with-nextflow.html
+++ b/instructor/01-getting-started-with-nextflow.html
@@ -555,7 +555,7 @@ <h3 class="card-title">Objectives</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> Instructor Note </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>The nextflow scripts for each lesson episode are available in the
 <code>scripts</code> directory created during the course setup. You
@@ -689,7 +689,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>You should see output similar to the text shown below:</p>
 <div class="codewrapper">
diff --git a/instructor/03-channels.html b/instructor/03-channels.html
index 1c6f2fa3..2f78c03d 100644
--- a/instructor/03-channels.html
+++ b/instructor/03-channels.html
@@ -490,7 +490,7 @@ <h3 class="callout-title">Queue vs Value Channel.<a class="anchor" aria-label="a
 <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">
 <ol style="list-style-type: decimal"><li>A queue channels is used to store multiple values.</li>
 <li>A value channel is used to store a single value, this can be a list
@@ -505,7 +505,7 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 <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> Instructor Note </h3>
 </button>
-<div id="collapseInstructor1" class="accordion-collapse collapse" data-bs-parent="#accordionInstructor1" aria-labelledby="headingInstructor1">
+<div id="collapseInstructor1" class="accordion-collapse collapse" aria-labelledby="headingInstructor1" data-bs-parent="#accordionInstructor1">
 <div class="accordion-body">
 <p>Create a nextflow script called to <code>channel.nf</code> for the
 following examples. Explain that as you are just setting up channels you
@@ -679,7 +679,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb10">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -767,7 +767,7 @@ <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"><
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" 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">
 <div class="codewrapper sourceCode" id="cb15">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -945,7 +945,7 @@ <h3 class="callout-title">Using Channel.fromPath<a class="anchor" aria-label="an
 <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" 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">
 <div class="codewrapper sourceCode" id="cb25">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1114,7 +1114,7 @@ <h3 class="callout-title">Create a channel containing groups of files<a class="a
 <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" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb31">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1135,66 +1135,6 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 </div>
 </div>
-</div>
-<div class="section level3">
-<h3 id="the-fromsra-channel-factory">The <strong>fromSRA</strong> Channel factory<a class="anchor" aria-label="anchor" href="#the-fromsra-channel-factory"></a></h3>
-<p>Another useful factory method is <code>fromSRA</code>. The
-<code>fromSRA</code> method makes it possible to query the <a href="https://www.ncbi.nlm.nih.gov/sra" class="external-link">NCBI SRA</a> archive and returns
-a queue channel emitting the FASTQ files matching the specified
-selection criteria.</p>
-<p>The queries can be project IDs or accession numbers supported by the
-<a href="https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ESearch" class="external-link">NCBI
-ESearch API</a>.</p>
-<p>If you want to use this functionality, you will need an <a href="https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/" class="external-link">NCBI
-API KEY</a>, and to set the environment variable
-<code>NCBI_API_KEY</code> to its value.</p>
-<div class="codewrapper sourceCode" id="cb33">
-<h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="sourceCode groovy" tabindex="0"><code class="sourceCode groovy"><span id="cb33-1"><a href="#cb33-1" tabindex="-1"></a>sra_ch <span class="op">=</span><span class="bu">Channel</span><span class="op">.</span><span class="fu">fromSRA</span><span class="op">(</span><span class="st">'SRP043510'</span><span class="op">)</span></span>
-<span id="cb33-2"><a href="#cb33-2" tabindex="-1"></a>sra_ch<span class="op">.</span><span class="fu">view</span><span class="op">()</span></span></code></pre>
-</div>
-<p>This will print a tuple for every fastq file associated with that SRA
-project accession.</p>
-<div class="codewrapper">
-<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="output" tabindex="0"><code>[SRR1448794, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR144/004/SRR1448794/SRR1448794.fastq.gz]
-[SRR1448795, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR144/005/SRR1448795/SRR1448795.fastq.gz]
-[SRR1448792, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR144/002/SRR1448792/SRR1448792.fastq.gz]
-[SRR1448793, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR144/003/SRR1448793/SRR1448793.fastq.gz]
-[SRR1910483, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR191/003/SRR1910483/SRR1910483.fastq.gz]
-[SRR1910482, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR191/002/SRR1910482/SRR1910482.fastq.gz]
-(remaining omitted)</code></pre>
-</div>
-<p>Multiple accession IDs can be specified using a list object:</p>
-<div class="codewrapper sourceCode" id="cb35">
-<h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="sourceCode groovy" tabindex="0"><code class="sourceCode groovy"><span id="cb35-1"><a href="#cb35-1" tabindex="-1"></a>ids <span class="op">=</span> <span class="op">[</span><span class="st">'ERR908507'</span><span class="op">,</span> <span class="st">'ERR908506'</span><span class="op">,</span> <span class="st">'ERR908505'</span><span class="op">]</span></span>
-<span id="cb35-2"><a href="#cb35-2" tabindex="-1"></a>sra_ch <span class="op">=</span> <span class="bu">Channel</span><span class="op">.</span><span class="fu">fromSRA</span><span class="op">(</span>ids<span class="op">)</span></span>
-<span id="cb35-3"><a href="#cb35-3" tabindex="-1"></a>sra_ch<span class="op">.</span><span class="fu">view</span><span class="op">()</span></span></code></pre>
-</div>
-<div class="codewrapper">
-<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="output" tabindex="0"><code>[ERR908507, [ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908507/ERR908507_1.fastq.gz, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908507/ERR908507_2.fastq.gz]]
-[ERR908506, [ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908506/ERR908506_1.fastq.gz, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908506/ERR908506_2.fastq.gz]]
-[ERR908505, [ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908505/ERR908505_1.fastq.gz, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908505/ERR908505_2.fastq.gz]]</code></pre>
-</div>
-<div id="read-pairs-from-sra" class="callout">
-<div class="callout-square">
-<i class="callout-icon" data-feather="bell"></i>
-</div>
-<div id="read-pairs-from-sra" class="callout-inner">
-<h3 class="callout-title">Read pairs from SRA<a class="anchor" aria-label="anchor" href="#read-pairs-from-sra"></a>
-</h3>
-<div class="callout-content">
-<p>Read pairs are implicitly managed, and are returned as a list of
-files.</p>
-</div>
-</div>
-</div>
 <div id="keypoints1" class="callout keypoints">
 <div class="callout-square">
 <i class="callout-icon" data-feather="key"></i>
diff --git a/instructor/12-nfcore.html b/instructor/12-nfcore.html
index 4311b5b0..13363255 100644
--- a/instructor/12-nfcore.html
+++ b/instructor/12-nfcore.html
@@ -679,7 +679,7 @@ <h3 class="callout-title">Exercise: listing nf-core pipelines<a class="anchor" a
 <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>Use the <code>--help</code> flag to print the list command usage.</p>
 <div class="codewrapper sourceCode" id="cb9">
@@ -803,7 +803,7 @@ <h3 class="callout-title">Exercise: Fetch the latest RNA-Seq pipeline<a class="a
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <p>Use the <code>nextflow pull</code> command to download the latest
 <code>nf-core/rnaseq</code> pipeline</p>
@@ -913,7 +913,7 @@ <h3 class="callout-title">Exercise : Create nf-core params file<a class="anchor"
 <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">
 <div class="codewrapper sourceCode" id="cb21">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1036,7 +1036,7 @@ <h3 class="callout-title">Exercise create a custom config<a class="anchor" aria-
 <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" 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>A line similar to one below in the file custom.config</p>
 <pre><code><span><span class="va">params.email</span> <span class="op">=</span> <span class="st">"myemail@address.com"</span></span></code></pre>
@@ -1158,7 +1158,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#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" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
 <div class="accordion-body">
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
diff --git a/instructor/aio.html b/instructor/aio.html
index 71e50f67..5f9d9d27 100644
--- a/instructor/aio.html
+++ b/instructor/aio.html
@@ -628,7 +628,7 @@ <h3 class="card-title">Objectives</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> Instructor Note </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>The nextflow scripts for each lesson episode are available in the
 <code>scripts</code> directory created during the course setup. You
@@ -765,7 +765,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution1" aria-expanded="false" aria-controls="collapseSolution1">
   <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 </button>
-<div id="collapseSolution1" class="accordion-collapse collapse" aria-labelledby="headingSolution1" data-bs-parent="#accordionSolution1">
+<div id="collapseSolution1" class="accordion-collapse collapse" data-bs-parent="#accordionSolution1" aria-labelledby="headingSolution1">
 <div class="accordion-body">
 <p>You should see output similar to the text shown below:</p>
 <div class="codewrapper">
@@ -1330,7 +1330,7 @@ <h3 class="callout-title">Queue vs Value Channel.<a class="anchor" aria-label="a
 <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">
 <ol style="list-style-type: decimal">
 <li>A queue channels is used to store multiple values.</li>
@@ -1347,7 +1347,7 @@ <h4 class="accordion-header" id="headingSolution1"> Show me the solution </h4>
 <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> Instructor Note </h3>
 </button>
-<div id="collapseInstructor1" class="accordion-collapse collapse" data-bs-parent="#accordionInstructor1" aria-labelledby="headingInstructor1">
+<div id="collapseInstructor1" class="accordion-collapse collapse" aria-labelledby="headingInstructor1" data-bs-parent="#accordionInstructor1">
 <div class="accordion-body">
 <p>Create a nextflow script called to <code>channel.nf</code> for the
 following examples. Explain that as you are just setting up channels you
@@ -1535,7 +1535,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb10">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1624,7 +1624,7 @@ <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"><
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution3" aria-expanded="false" aria-controls="collapseSolution3">
   <h4 class="accordion-header" id="headingSolution3"> Show me the solution </h4>
 </button>
-<div id="collapseSolution3" class="accordion-collapse collapse" 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">
 <div class="codewrapper sourceCode" id="cb15">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -1831,7 +1831,7 @@ <h3 class="callout-title">Using Channel.fromPath<a class="anchor" aria-label="an
 <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" 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">
 <div class="codewrapper sourceCode" id="cb25">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -2037,7 +2037,7 @@ <h3 class="callout-title">Create a channel containing groups of files<a class="a
 <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" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
 <div class="accordion-body">
 <div class="codewrapper sourceCode" id="cb31">
 <h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -2058,67 +2058,6 @@ <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"><
 </div>
 </div>
 </div>
-</div>
-<div class="section level3">
-<h3 id="the-fromsra-channel-factory">The <strong>fromSRA</strong> Channel factory<a class="anchor" aria-label="anchor" href="#the-fromsra-channel-factory"></a>
-</h3>
-<p>Another useful factory method is <code>fromSRA</code>. The
-<code>fromSRA</code> method makes it possible to query the <a href="https://www.ncbi.nlm.nih.gov/sra" class="external-link">NCBI SRA</a> archive and returns
-a queue channel emitting the FASTQ files matching the specified
-selection criteria.</p>
-<p>The queries can be project IDs or accession numbers supported by the
-<a href="https://www.ncbi.nlm.nih.gov/books/NBK25499/#chapter4.ESearch" class="external-link">NCBI
-ESearch API</a>.</p>
-<p>If you want to use this functionality, you will need an <a href="https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/" class="external-link">NCBI
-API KEY</a>, and to set the environment variable
-<code>NCBI_API_KEY</code> to its value.</p>
-<div class="codewrapper sourceCode" id="cb33">
-<h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="sourceCode groovy" tabindex="0"><code class="sourceCode groovy"><span id="cb33-1"><a href="#cb33-1" tabindex="-1"></a>sra_ch <span class="op">=</span><span class="bu">Channel</span><span class="op">.</span><span class="fu">fromSRA</span><span class="op">(</span><span class="st">'SRP043510'</span><span class="op">)</span></span>
-<span id="cb33-2"><a href="#cb33-2" tabindex="-1"></a>sra_ch<span class="op">.</span><span class="fu">view</span><span class="op">()</span></span></code></pre>
-</div>
-<p>This will print a tuple for every fastq file associated with that SRA
-project accession.</p>
-<div class="codewrapper">
-<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="output" tabindex="0"><code>[SRR1448794, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR144/004/SRR1448794/SRR1448794.fastq.gz]
-[SRR1448795, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR144/005/SRR1448795/SRR1448795.fastq.gz]
-[SRR1448792, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR144/002/SRR1448792/SRR1448792.fastq.gz]
-[SRR1448793, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR144/003/SRR1448793/SRR1448793.fastq.gz]
-[SRR1910483, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR191/003/SRR1910483/SRR1910483.fastq.gz]
-[SRR1910482, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR191/002/SRR1910482/SRR1910482.fastq.gz]
-(remaining omitted)</code></pre>
-</div>
-<p>Multiple accession IDs can be specified using a list object:</p>
-<div class="codewrapper sourceCode" id="cb35">
-<h3 class="code-label">GROOVY<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="sourceCode groovy" tabindex="0"><code class="sourceCode groovy"><span id="cb35-1"><a href="#cb35-1" tabindex="-1"></a>ids <span class="op">=</span> <span class="op">[</span><span class="st">'ERR908507'</span><span class="op">,</span> <span class="st">'ERR908506'</span><span class="op">,</span> <span class="st">'ERR908505'</span><span class="op">]</span></span>
-<span id="cb35-2"><a href="#cb35-2" tabindex="-1"></a>sra_ch <span class="op">=</span> <span class="bu">Channel</span><span class="op">.</span><span class="fu">fromSRA</span><span class="op">(</span>ids<span class="op">)</span></span>
-<span id="cb35-3"><a href="#cb35-3" tabindex="-1"></a>sra_ch<span class="op">.</span><span class="fu">view</span><span class="op">()</span></span></code></pre>
-</div>
-<div class="codewrapper">
-<h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
-</h3>
-<pre class="output" tabindex="0"><code>[ERR908507, [ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908507/ERR908507_1.fastq.gz, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908507/ERR908507_2.fastq.gz]]
-[ERR908506, [ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908506/ERR908506_1.fastq.gz, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908506/ERR908506_2.fastq.gz]]
-[ERR908505, [ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908505/ERR908505_1.fastq.gz, ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR908/ERR908505/ERR908505_2.fastq.gz]]</code></pre>
-</div>
-<div id="read-pairs-from-sra" class="callout">
-<div class="callout-square">
-<i class="callout-icon" data-feather="bell"></i>
-</div>
-<div id="read-pairs-from-sra" class="callout-inner">
-<h3 class="callout-title">Read pairs from SRA<a class="anchor" aria-label="anchor" href="#read-pairs-from-sra"></a>
-</h3>
-<div class="callout-content">
-<p>Read pairs are implicitly managed, and are returned as a list of
-files.</p>
-</div>
-</div>
-</div>
 <div id="keypoints1" class="callout keypoints">
 <div class="callout-square">
 <i class="callout-icon" data-feather="key"></i>
@@ -9595,7 +9534,7 @@ <h3 class="callout-title">Exercise: listing nf-core pipelines<a class="anchor" a
 <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>Use the <code>--help</code> flag to print the list command usage.</p>
 <div class="codewrapper sourceCode" id="cb9">
@@ -9724,7 +9663,7 @@ <h3 class="callout-title">Exercise: Fetch the latest RNA-Seq pipeline<a class="a
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#collapseSolution2" aria-expanded="false" aria-controls="collapseSolution2">
   <h4 class="accordion-header" id="headingSolution2"> Show me the solution </h4>
 </button>
-<div id="collapseSolution2" class="accordion-collapse collapse" data-bs-parent="#accordionSolution2" aria-labelledby="headingSolution2">
+<div id="collapseSolution2" class="accordion-collapse collapse" aria-labelledby="headingSolution2" data-bs-parent="#accordionSolution2">
 <div class="accordion-body">
 <p>Use the <code>nextflow pull</code> command to download the latest
 <code>nf-core/rnaseq</code> pipeline</p>
@@ -9839,7 +9778,7 @@ <h3 class="callout-title">Exercise : Create nf-core params file<a class="anchor"
 <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">
 <div class="codewrapper sourceCode" id="cb21">
 <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
@@ -9978,7 +9917,7 @@ <h3 class="callout-title">Exercise create a custom config<a class="anchor" aria-
 <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" 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>A line similar to one below in the file custom.config</p>
 <pre><code><span><span class="va">params.email</span> <span class="op">=</span> <span class="st">"myemail@address.com"</span></span></code></pre>
@@ -10103,7 +10042,7 @@ <h3 class="code-label">BASH<i aria-hidden="true" data-feather="chevron-left"></i
 <button class="accordion-button solution-button collapsed" type="button" data-bs-toggle="collapse" data-bs-target="#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" data-bs-parent="#accordionSolution5" aria-labelledby="headingSolution5">
+<div id="collapseSolution5" class="accordion-collapse collapse" aria-labelledby="headingSolution5" data-bs-parent="#accordionSolution5">
 <div class="accordion-body">
 <div class="codewrapper">
 <h3 class="code-label">OUTPUT<i aria-hidden="true" data-feather="chevron-left"></i><i aria-hidden="true" data-feather="chevron-right"></i>
diff --git a/md5sum.txt b/md5sum.txt
index 7f6136ec..bf0ae8c2 100644
--- a/md5sum.txt
+++ b/md5sum.txt
@@ -5,7 +5,7 @@
 "index.md" "87e5c1aef0986cad40b8a1b74ac0a421" "site/built/index.md" "2024-04-23"
 "episodes/01-getting-started-with-nextflow.md" "5d1a504430d8c242185d119b42d257d1" "site/built/01-getting-started-with-nextflow.md" "2024-06-10"
 "episodes/02-workflow_parameters.md" "d23890eae0238c497616146440022320" "site/built/02-workflow_parameters.md" "2024-08-23"
-"episodes/03-channels.md" "bfc8f5bccd23669481f0c802f68a48fc" "site/built/03-channels.md" "2024-08-23"
+"episodes/03-channels.md" "b5fad65581aa51e318f8050e3e61dc2e" "site/built/03-channels.md" "2024-08-23"
 "episodes/04-processes-part1.md" "54f85d225365caded8db61dd5e53be9c" "site/built/04-processes-part1.md" "2024-07-23"
 "episodes/05-processes-part2.md" "b5b93cff0e547801572e8f3f4c5713f7" "site/built/05-processes-part2.md" "2024-06-10"
 "episodes/06-workflow.md" "9fa328c536dab560c108b897320a8e9a" "site/built/06-workflow.md" "2024-06-10"
diff --git a/pkgdown.yml b/pkgdown.yml
index b5641df9..c8ba415f 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,4 +2,4 @@ pandoc: 3.1.11
 pkgdown: 2.1.0
 pkgdown_sha: ~
 articles: {}
-last_built: 2024-08-23T08:39Z
+last_built: 2024-08-23T08:49Z