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@@ -54,7 +54,7 @@
                                 <img class="max-h-10 hidden dark:inline-block" src="/HARPY/static/favicon.png">
                             </span>
                             <span class="dark:text-white font-semibold line-clamp-1 md:line-clamp-2">Harpy</span>
-                        </a><span class="hidden px-2 py-1 ml-4 text-sm font-semibold leading-none text-root-logo-label-text bg-root-logo-label-bg rounded-sm md:inline-block">v0.4.0</span>
+                        </a><span class="hidden px-2 py-1 ml-4 text-sm font-semibold leading-none text-root-logo-label-text bg-root-logo-label-bg rounded-sm md:inline-block">v0.5.0</span>
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diff --git a/commonoptions/index.html b/commonoptions/index.html
@@ -4,7 +4,7 @@
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@@ -58,7 +58,7 @@
                                 <img class="max-h-10 hidden dark:inline-block" src="../static/favicon.png">
                             </span>
                             <span class="dark:text-white font-semibold line-clamp-1 md:line-clamp-2">Harpy</span>
-                        </a><span class="hidden px-2 py-1 ml-4 text-sm font-semibold leading-none text-root-logo-label-text bg-root-logo-label-bg rounded-sm md:inline-block">v0.4.0</span>
+                        </a><span class="hidden px-2 py-1 ml-4 text-sm font-semibold leading-none text-root-logo-label-text bg-root-logo-label-bg rounded-sm md:inline-block">v0.5.0</span>
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                     <span class="hidden h-8 border-r md:inline-block dark:border-dark-650"></span>
@@ -230,6 +230,12 @@ <h1>
         <span><svg xmlns="http://www.w3.org/2000/svg" class="docs-icon" viewBox="0 0 24 24" role="presentation"><g fill="currentColor"><g><path d="M8.75 5.5h11.5a.75.75 0 0 1 0 1.5H8.75a.75.75 0 0 1 0-1.5Zm0 6h11.5a.75.75 0 0 1 0 1.5H8.75a.75.75 0 0 1 0-1.5Zm0 6h11.5a.75.75 0 0 1 0 1.5H8.75a.75.75 0 0 1 0-1.5ZM5 12a1 1 0 1 1-2 0 1 1 0 0 1 2 0ZM4 7a1 1 0 1 1 0-2 1 1 0 0 1 0 2Zm0 12a1 1 0 1 1 0-2 1 1 0 0 1 0 2Z"/></g></g></svg> Common Harpy Options</span>
     </h1>
 </doc-anchor-target>
+<doc-anchor-target id="common-command-line-options">
+    <h2>
+        <doc-anchor-trigger class="header-anchor-trigger" to="#common-command-line-options">#</doc-anchor-trigger>
+        <span>Common command-line options</span>
+    </h2>
+</doc-anchor-target>
 <p>Every Harpy module has a series of configuration parameters. These are arguments you need to input
 to configure the module to run on your data, such as the directory with the reads/alignments,
 the genome assembly, etc. All main modules (e.g. <code v-pre>qc</code>) also share a series of common runtime
@@ -258,6 +264,22 @@ <h1>
 <td style="text-align: left;">Number of threads to use</td>
 </tr>
 <tr>
+<td style="text-align: left;"><code v-pre>--print-only</code></td>
+<td style="text-align: center;"></td>
+<td style="text-align: left;">toggle</td>
+<td style="text-align: center;"></td>
+<td style="text-align: center;">no</td>
+<td style="text-align: left;">Perform internal validations, build the workflow environment, and print the resulting Snakemake command, but don&#x27;t run anything</td>
+</tr>
+<tr>
+<td style="text-align: left;"><code v-pre>--skipreports</code></td>
+<td style="text-align: center;"><code v-pre>-r</code></td>
+<td style="text-align: left;">toggle</td>
+<td style="text-align: center;"></td>
+<td style="text-align: center;">no</td>
+<td style="text-align: left;">Skip the processing and generation of HTML reports in a workflow</td>
+</tr>
+<tr>
 <td style="text-align: left;"><code v-pre>--snakemake</code></td>
 <td style="text-align: center;"><code v-pre>-s</code></td>
 <td style="text-align: left;">string</td>
@@ -292,6 +314,49 @@ <h1>
 
 harpy align bwa -t 20 -d samples/trimmedreads -q</code></pre>
 </doc-codeblock></div>
+<doc-anchor-target id="the-workflow-folder">
+    <h2>
+        <doc-anchor-trigger class="header-anchor-trigger" to="#the-workflow-folder">#</doc-anchor-trigger>
+        <span>The <code v-pre>workflow</code> folder</span>
+    </h2>
+</doc-anchor-target>
+<p>When you run one of the main Harpy modules, the output directory will contain a <code v-pre>workflow</code> folder. This folder is
+both necessary for the module to run and is very useful to understand what the module did, be it for your own
+understanding or as a point of reference when writing the Methods within a manuscript. The presence of the folder
+and the contents therein also allow you to rerun the workflow manually. The <code v-pre>workflow</code> folder may contain the following:</p>
+<div class="table-wrapper scrollbar overflow-hidden">
+<table class="comfortable">
+<thead>
+<tr>
+<th style="text-align: left;">item</th>
+<th style="text-align: left;">contents</th>
+<th style="text-align: left;">utility</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+<td style="text-align: left;"><code v-pre>*.smk</code></td>
+<td style="text-align: left;">Snakefile with the full recipe of the workflow</td>
+<td style="text-align: left;">useful for understanding the workflow</td>
+</tr>
+<tr>
+<td style="text-align: left;"><code v-pre>config.yml</code></td>
+<td style="text-align: left;">Configuration file generated from command-line arguments and consumed by the Snakefile</td>
+<td style="text-align: left;">useful for bookkeeping</td>
+</tr>
+<tr>
+<td style="text-align: left;"><code v-pre>report/*.Rmd</code></td>
+<td style="text-align: left;">RMarkdown files used to generate the fancy reports</td>
+<td style="text-align: left;">useful to understand math behind plots/tables or borrow code from</td>
+</tr>
+<tr>
+<td style="text-align: left;"><code v-pre>*.workflow.summary</code></td>
+<td style="text-align: left;">Plain-text overview of the important parts of the workflow</td>
+<td style="text-align: left;">useful for bookkeeping and writing Methods</td>
+</tr>
+</tbody>
+</table>
+</div>
 <doc-anchor-target id="the-genome-folder">
     <h2>
         <doc-anchor-trigger class="header-anchor-trigger" to="#the-genome-folder">#</doc-anchor-trigger>

diff --git a/development/index.html b/development/index.html
@@ -4,7 +4,7 @@
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@@ -60,7 +60,7 @@
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                             </span>
                             <span class="dark:text-white font-semibold line-clamp-1 md:line-clamp-2">Harpy</span>
-                        </a><span class="hidden px-2 py-1 ml-4 text-sm font-semibold leading-none text-root-logo-label-text bg-root-logo-label-bg rounded-sm md:inline-block">v0.4.0</span>
+                        </a><span class="hidden px-2 py-1 ml-4 text-sm font-semibold leading-none text-root-logo-label-text bg-root-logo-label-bg rounded-sm md:inline-block">v0.5.0</span>
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diff --git a/haplotagdata/index.html b/haplotagdata/index.html
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@@ -32,11 +32,11 @@
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     <link href="../static/favicon.png" rel="icon">
-    <link href="../resources/css/retype.css?v=3.5.0.760737878453" rel="stylesheet">
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-    <script data-cfasync="false" src="../resources/js/config.js?v=3.5.0.760737878453" data-turbo-eval="false" defer></script>
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@@ -59,7 +59,7 @@
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                             </span>
                             <span class="dark:text-white font-semibold line-clamp-1 md:line-clamp-2">Harpy</span>
-                        </a><span class="hidden px-2 py-1 ml-4 text-sm font-semibold leading-none text-root-logo-label-text bg-root-logo-label-bg rounded-sm md:inline-block">v0.4.0</span>
+                        </a><span class="hidden px-2 py-1 ml-4 text-sm font-semibold leading-none text-root-logo-label-text bg-root-logo-label-bg rounded-sm md:inline-block">v0.5.0</span>
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diff --git a/index.html b/index.html
@@ -4,7 +4,7 @@
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@@ -59,7 +59,7 @@
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                             </span>
                             <span class="dark:text-white font-semibold line-clamp-1 md:line-clamp-2">Harpy</span>
-                        </a><span class="hidden px-2 py-1 ml-4 text-sm font-semibold leading-none text-root-logo-label-text bg-root-logo-label-bg rounded-sm md:inline-block">v0.4.0</span>
+                        </a><span class="hidden px-2 py-1 ml-4 text-sm font-semibold leading-none text-root-logo-label-text bg-root-logo-label-bg rounded-sm md:inline-block">v0.5.0</span>
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