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diff --git a/haplotagdata/index.html b/haplotagdata/index.html
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diff --git a/install/index.html b/install/index.html
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diff --git a/issues/index.html b/issues/index.html
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diff --git a/modules/align/bwa/index.html b/modules/align/bwa/index.html
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+    <script id="lunr-js" data-cfasync="false" src="../../../resources/js/lunr.js?v=3.5.0.770910636470" data-turbo-eval="false" defer></script>
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@@ -407,25 +407,27 @@ <h2>
 The <code v-pre>BX:Z</code> tags in the read headers are still added to the alignment headers, even though barcodes
 are not used to inform mapping. The <code v-pre>-m</code> threshold is used for alignment molecule assignment.</p>
 <div class="overflow-hidden mb-6 py-4 dark:px-5 dark:bg-white rounded-md"><pre class="mermaid w-full">graph LR
-    A([index genome]) --&gt; B([align to genome])
-    B--&gt;C([sort alignments])
-    C--&gt;D([mark duplicates])
-    D--&gt;E([assign molecules])
-    E--&gt;F([alignment metrics])
-    D--&gt;G([barcode stats])
+    A([index genome]):::clean --&gt; B([align to genome]):::clean
+    B--&gt;C([sort alignments]):::clean
+    C--&gt;D([mark duplicates]):::clean
+    D--&gt;E([assign molecules]):::clean
+    E--&gt;F([alignment metrics]):::clean
+    D--&gt;G([barcode stats]):::clean
     G--&gt;F
     subgraph aln [Inputs]
-        Z[FASTQ files]---genome
+        Z[FASTQ files]:::clean---genome:::clean
     end
     aln--&gt;B &amp; A
     subgraph markdp [mark duplicates via `samtools`]
         direction LR
-        collate--&gt;fixmate
-        fixmate--&gt;sort
-        sort--&gt;markdup
+        collate:::clean--&gt;fixmate:::clean
+        fixmate--&gt;sort:::clean
+        sort--&gt;markdup:::clean
     end
     style markdp fill:#f0f0f0,stroke:#e8e8e8,stroke-width:2px
-    style aln fill:#f0f0f0,stroke:#e8e8e8,stroke-width:2px</pre></div>
+    style aln fill:#f0f0f0,stroke:#e8e8e8,stroke-width:2px
+    classDef clean fill:#f5f6f9,stroke:#b7c9ef,stroke-width:2px
+</pre></div>
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