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diff --git a/404.html b/404.html
@@ -4,7 +4,7 @@
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@@ -29,11 +29,11 @@
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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">v0.7.x</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">v0.8.x</span>
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diff --git a/commonoptions/index.html b/commonoptions/index.html
@@ -4,7 +4,7 @@
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-    <meta name="turbo-cache-control" content="no-cache" data-turbo-track="reload" data-track-token="3.5.0.762624045714">
+    <meta name="turbo-cache-control" content="no-cache" data-turbo-track="reload" data-track-token="3.5.0.764430853810">
 
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@@ -32,12 +32,12 @@
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     <link href="../static/favicon.png" rel="icon">
-    <link href="../resources/css/retype.css?v=3.5.0.762624045714" rel="stylesheet">
+    <link href="../resources/css/retype.css?v=3.5.0.764430853810" rel="stylesheet">
 
-    <script data-cfasync="false" src="../resources/js/config.js?v=3.5.0.762624045714" data-turbo-eval="false" defer></script>
+    <script data-cfasync="false" src="../resources/js/config.js?v=3.5.0.764430853810" data-turbo-eval="false" defer></script>
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+    <script id="lunr-js" data-cfasync="false" src="../resources/js/lunr.js?v=3.5.0.764430853810" data-turbo-eval="false" defer></script>
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 </head>
 <body>
     <div id="docs-app" class="relative text-base antialiased text-gray-700 bg-white font-body dark:bg-dark-850 dark:text-dark-300">
@@ -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">v0.7.x</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">v0.8.x</span>
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                     <span class="hidden h-8 border-r md:inline-block dark:border-dark-650"></span>
@@ -317,6 +317,14 @@ <h2>
 </thead>
 <tbody>
 <tr>
+<td style="text-align: left;"><code v-pre>--output-dir</code></td>
+<td style="text-align: center;"><code v-pre>-o</code></td>
+<td style="text-align: left;">string</td>
+<td style="text-align: center;">varies</td>
+<td style="text-align: center;">no</td>
+<td style="text-align: left;">Name of output directory</td>
+</tr>
+<tr>
 <td style="text-align: left;"><code v-pre>--threads</code></td>
 <td style="text-align: center;"><code v-pre>-t</code></td>
 <td style="text-align: left;">integer</td>
@@ -325,14 +333,6 @@ <h2>
 <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>

diff --git a/development/index.html b/development/index.html
@@ -4,7 +4,7 @@
     <meta charset="UTF-8">
     <meta name="viewport" content="width=device-width,initial-scale=1">
     <meta name="turbo-root" content="/HARPY">
-    <meta name="turbo-cache-control" content="no-cache" data-turbo-track="reload" data-track-token="3.5.0.762624045714">
+    <meta name="turbo-cache-control" content="no-cache" data-turbo-track="reload" data-track-token="3.5.0.764430853810">
 
     <!-- See retype.com -->
     <meta name="generator" content="Retype 3.5.0">
@@ -34,12 +34,12 @@
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     <link href="../static/favicon.png" rel="icon">
-    <link href="../resources/css/retype.css?v=3.5.0.762624045714" rel="stylesheet">
+    <link href="../resources/css/retype.css?v=3.5.0.764430853810" rel="stylesheet">
 
-    <script data-cfasync="false" src="../resources/js/config.js?v=3.5.0.762624045714" data-turbo-eval="false" defer></script>
+    <script data-cfasync="false" src="../resources/js/config.js?v=3.5.0.764430853810" data-turbo-eval="false" defer></script>
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+    <script id="lunr-js" data-cfasync="false" src="../resources/js/lunr.js?v=3.5.0.764430853810" data-turbo-eval="false" defer></script>
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 </head>
 <body>
     <div id="docs-app" class="relative text-base antialiased text-gray-700 bg-white font-body dark:bg-dark-850 dark:text-dark-300">
@@ -60,7 +60,7 @@
                                 <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">v0.7.x</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">v0.8.x</span>
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                     <span class="hidden h-8 border-r md:inline-block dark:border-dark-650"></span>

diff --git a/haplotagdata/index.html b/haplotagdata/index.html
@@ -4,7 +4,7 @@
     <meta charset="UTF-8">
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-    <meta name="turbo-cache-control" content="no-cache" data-turbo-track="reload" data-track-token="3.5.0.762624045714">
+    <meta name="turbo-cache-control" content="no-cache" data-turbo-track="reload" data-track-token="3.5.0.764430853810">
 
     <!-- See retype.com -->
     <meta name="generator" content="Retype 3.5.0">
@@ -34,11 +34,11 @@
     <script data-cfasync="false">(function () { var el = document.documentElement, m = localStorage.getItem("doc_theme"), wm = window.matchMedia; if (m === "dark" || (!m && wm && wm("(prefers-color-scheme: dark)").matches)) { el.classList.add("dark") } else { el.classList.remove("dark") } })();</script>
 
     <link href="../static/favicon.png" rel="icon">
-    <link href="../resources/css/retype.css?v=3.5.0.762624045714" rel="stylesheet">
+    <link href="../resources/css/retype.css?v=3.5.0.764430853810" rel="stylesheet">
 
-    <script data-cfasync="false" src="../resources/js/config.js?v=3.5.0.762624045714" data-turbo-eval="false" defer></script>
+    <script data-cfasync="false" src="../resources/js/config.js?v=3.5.0.764430853810" data-turbo-eval="false" defer></script>
     <script data-cfasync="false" src="../resources/js/retype.js?v=3.5.0" data-turbo-eval="false" defer></script>
-    <script id="lunr-js" data-cfasync="false" src="../resources/js/lunr.js?v=3.5.0.762624045714" data-turbo-eval="false" defer></script>
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 </head>
@@ -61,7 +61,7 @@
                                 <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">v0.7.x</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">v0.8.x</span>
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                     <span class="hidden h-8 border-r md:inline-block dark:border-dark-650"></span>

diff --git a/index.html b/index.html
@@ -4,7 +4,7 @@
     <meta charset="UTF-8">
     <meta name="viewport" content="width=device-width,initial-scale=1">
     <meta name="turbo-root" content="/HARPY">
-    <meta name="turbo-cache-control" content="no-cache" data-turbo-track="reload" data-track-token="3.5.0.762624045714">
+    <meta name="turbo-cache-control" content="no-cache" data-turbo-track="reload" data-track-token="3.5.0.764430853810">
 
     <!-- See retype.com -->
     <meta name="generator" content="Retype 3.5.0">
@@ -34,11 +34,11 @@
     <script data-cfasync="false">(function () { var el = document.documentElement, m = localStorage.getItem("doc_theme"), wm = window.matchMedia; if (m === "dark" || (!m && wm && wm("(prefers-color-scheme: dark)").matches)) { el.classList.add("dark") } else { el.classList.remove("dark") } })();</script>
 
     <link href="static/favicon.png" rel="icon">
-    <link href="resources/css/retype.css?v=3.5.0.762624045714" rel="stylesheet">
+    <link href="resources/css/retype.css?v=3.5.0.764430853810" rel="stylesheet">
 
-    <script data-cfasync="false" src="resources/js/config.js?v=3.5.0.762624045714" data-turbo-eval="false" defer></script>
+    <script data-cfasync="false" src="resources/js/config.js?v=3.5.0.764430853810" data-turbo-eval="false" defer></script>
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-    <script id="lunr-js" data-cfasync="false" src="resources/js/lunr.js?v=3.5.0.762624045714" data-turbo-eval="false" defer></script>
+    <script id="lunr-js" data-cfasync="false" src="resources/js/lunr.js?v=3.5.0.764430853810" data-turbo-eval="false" defer></script>
 </head>
 <body>
     <div id="docs-app" class="relative text-base antialiased text-gray-700 bg-white font-body dark:bg-dark-850 dark:text-dark-300">
@@ -59,7 +59,7 @@
                                 <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">v0.7.x</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">v0.8.x</span>
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                     <span class="hidden h-8 border-r md:inline-block dark:border-dark-650"></span>

diff --git a/install/index.html b/install/index.html
@@ -4,7 +4,7 @@
     <meta charset="UTF-8">
     <meta name="viewport" content="width=device-width,initial-scale=1">
     <meta name="turbo-root" content="/HARPY">
-    <meta name="turbo-cache-control" content="no-cache" data-turbo-track="reload" data-track-token="3.5.0.762624045714">
+    <meta name="turbo-cache-control" content="no-cache" data-turbo-track="reload" data-track-token="3.5.0.764430853810">
 
     <!-- See retype.com -->
     <meta name="generator" content="Retype 3.5.0">
@@ -32,12 +32,12 @@
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     <link href="../static/favicon.png" rel="icon">
-    <link href="../resources/css/retype.css?v=3.5.0.762624045714" rel="stylesheet">
+    <link href="../resources/css/retype.css?v=3.5.0.764430853810" rel="stylesheet">
 
-    <script data-cfasync="false" src="../resources/js/config.js?v=3.5.0.762624045714" data-turbo-eval="false" defer></script>
+    <script data-cfasync="false" src="../resources/js/config.js?v=3.5.0.764430853810" data-turbo-eval="false" defer></script>
     <script data-cfasync="false" src="../resources/js/retype.js?v=3.5.0" data-turbo-eval="false" defer></script>
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-    <script id="prism-js" data-cfasync="false" src="../resources/js/prism.js?v=3.5.0.762624045714" defer></script>
+    <script id="lunr-js" data-cfasync="false" src="../resources/js/lunr.js?v=3.5.0.764430853810" data-turbo-eval="false" defer></script>
+    <script id="prism-js" data-cfasync="false" src="../resources/js/prism.js?v=3.5.0.764430853810" defer></script>
 </head>
 <body>
     <div id="docs-app" class="relative text-base antialiased text-gray-700 bg-white font-body dark:bg-dark-850 dark:text-dark-300">
@@ -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">v0.7.x</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">v0.8.x</span>
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                     <span class="hidden h-8 border-r md:inline-block dark:border-dark-650"></span>