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development/contributors/index.html

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     <li class="wy-breadcrumbs-aside">
-          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/7b08e82f1079569fdad98e8f2ec973373f8095ae/README.md" class="icon icon-github"> Edit on GitHub</a>
+          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/7aaae3466345f0287d1cb5980a268d55dac24ec1/README.md" class="icon icon-github"> Edit on GitHub</a>
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development/discussions/index.html

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     <li><a href=".." class="icon icon-home" aria-label="Docs"></a></li>
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-          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/7b08e82f1079569fdad98e8f2ec973373f8095ae/README.md" class="icon icon-github"> Edit on GitHub</a>
+          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/7aaae3466345f0287d1cb5980a268d55dac24ec1/README.md" class="icon icon-github"> Edit on GitHub</a>
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development/flow-diagram/index.html

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-          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/7b08e82f1079569fdad98e8f2ec973373f8095ae/README.md" class="icon icon-github"> Edit on GitHub</a>
+          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/7aaae3466345f0287d1cb5980a268d55dac24ec1/README.md" class="icon icon-github"> Edit on GitHub</a>
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development/how-to-run/index.html

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     <li><a href=".." class="icon icon-home" aria-label="Docs"></a></li>
       <li class="breadcrumb-item active">How To Run</li>
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-          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/7b08e82f1079569fdad98e8f2ec973373f8095ae/README.md" class="icon icon-github"> Edit on GitHub</a>
+          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/7aaae3466345f0287d1cb5980a268d55dac24ec1/README.md" class="icon icon-github"> Edit on GitHub</a>
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@@ -111,10 +111,10 @@ <h2 id="how-to-run">How To Run</h2>
 <p><strong>The pipeline is currently configured to run on a SINGLE NODE mode with normal only, tumor only, normal-tumor paired, or multiple normal and tumor samples.</strong></p>
 <ol>
 <li>
-<p>Update the params section of the .config file (<a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/7b08e82f1079569fdad98e8f2ec973373f8095ae/config/template.config">Example config</a>).</p>
+<p>Update the params section of the .config file (<a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/7aaae3466345f0287d1cb5980a268d55dac24ec1/config/template.config">Example config</a>).</p>
 </li>
 <li>
-<p>Update the YAML (<a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/7b08e82f1079569fdad98e8f2ec973373f8095ae/input">Template YAMLs</a>).</p>
+<p>Update the YAML (<a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/7aaae3466345f0287d1cb5980a268d55dac24ec1/input">Template YAMLs</a>).</p>
 </li>
 <li>
 <p>Download the submission script (submit_nextflow_pipeline.py) from <a href="https://github.com/uclahs-cds/tool-submit-nf">here</a>, and submit your pipeline below.</p>

development/index.html

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     <li><a href="." class="icon icon-home" aria-label="Docs"></a></li>
       <li class="breadcrumb-item active">Home</li>
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-          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/7b08e82f1079569fdad98e8f2ec973373f8095ae/README.md" class="icon icon-github"> Edit on GitHub</a>
+          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/7aaae3466345f0287d1cb5980a268d55dac24ec1/README.md" class="icon icon-github"> Edit on GitHub</a>
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@@ -170,5 +170,5 @@ <h1 id="recalibrate-bam">recalibrate-BAM</h1>
 
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-Build Date UTC : 2024-10-08 23:52:23.877146+00:00
+Build Date UTC : 2024-10-09 00:13:15.269862+00:00
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development/inputs/index.html

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-          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/7b08e82f1079569fdad98e8f2ec973373f8095ae/README.md" class="icon icon-github"> Edit on GitHub</a>
+          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/7aaae3466345f0287d1cb5980a268d55dac24ec1/README.md" class="icon icon-github"> Edit on GitHub</a>
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-<p>The below parameters have default values defined in <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/7b08e82f1079569fdad98e8f2ec973373f8095ae/config/default.config"><code>default.config</code></a> and generally do not need to be set by the user.</p>
+<p>The below parameters have default values defined in <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/7aaae3466345f0287d1cb5980a268d55dac24ec1/config/default.config"><code>default.config</code></a> and generally do not need to be set by the user.</p>
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 <h4 id="base-resource-allocation-updaters">Base resource allocation updaters</h4>
-<p>To update the base resource (cpus or memory) allocations for processes, use the following structure and add the necessary parts. The default allocations can be found in the <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/7b08e82f1079569fdad98e8f2ec973373f8095ae/config">node-specific config files</a></p>
+<p>To update the base resource (cpus or memory) allocations for processes, use the following structure and add the necessary parts. The default allocations can be found in the <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/7aaae3466345f0287d1cb5980a268d55dac24ec1/config">node-specific config files</a></p>
 <pre><code class="language-Nextflow">base_resource_update {
     memory = [
         [['process_name', 'process_name2'], &lt;multiplier for resource&gt;],

development/license/index.html

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+          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/7aaae3466345f0287d1cb5980a268d55dac24ec1/README.md" class="icon icon-github"> Edit on GitHub</a>
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development/outputs/index.html

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-          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/7b08e82f1079569fdad98e8f2ec973373f8095ae/README.md" class="icon icon-github"> Edit on GitHub</a>
+          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/7aaae3466345f0287d1cb5980a268d55dac24ec1/README.md" class="icon icon-github"> Edit on GitHub</a>
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development/overview/index.html

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+          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/7aaae3466345f0287d1cb5980a268d55dac24ec1/README.md" class="icon icon-github"> Edit on GitHub</a>
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development/pipeline-steps/index.html

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+          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/7aaae3466345f0287d1cb5980a268d55dac24ec1/README.md" class="icon icon-github"> Edit on GitHub</a>
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development/references/index.html

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+          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/7aaae3466345f0287d1cb5980a268d55dac24ec1/README.md" class="icon icon-github"> Edit on GitHub</a>
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versions.json

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     "title": "development",
     "aliases": [],
     "properties": {
-      "commit": "7b08e82f1079569fdad98e8f2ec973373f8095ae",
-      "date": "2024-10-08T16:51:46-07:00"
+      "commit": "7aaae3466345f0287d1cb5980a268d55dac24ec1",
+      "date": "2024-10-08T17:12:38-07:00"
     }
   },
   {
     "version": "v1.0.1",
     "title": "v1.0.1",
     "aliases": [
-      "latest",
-      "release-candidate"
+      "release-candidate",
+      "latest"
     ],
     "properties": {
       "commit": "3ee8f38f845c29e06fcc5be02a00b091c2ab2c9e",