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uclahs-cds · May 17, 2024 · adf6322 · adf6322
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diff --git a/development/contributors/index.html b/development/contributors/index.html
@@ -98,7 +98,7 @@
     <li><a href=".." class="icon icon-home" aria-label="Docs"></a></li>
       <li class="breadcrumb-item active">Contributors</li>
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-          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/d71ba5e0e8ef346522695b8431a324a67acf0fab/README.md" class="icon icon-github"> Edit on GitHub</a>
+          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/1d736cdbe898a786b20b3b494d215c1a563a7574/README.md" class="icon icon-github"> Edit on GitHub</a>
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diff --git a/development/discussions/index.html b/development/discussions/index.html
@@ -98,7 +98,7 @@
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       <li class="breadcrumb-item active">Discussions</li>
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+          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/1d736cdbe898a786b20b3b494d215c1a563a7574/README.md" class="icon icon-github"> Edit on GitHub</a>
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diff --git a/development/flow-diagram/index.html b/development/flow-diagram/index.html
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       <li class="breadcrumb-item active">Flow Diagram</li>
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+          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/1d736cdbe898a786b20b3b494d215c1a563a7574/README.md" class="icon icon-github"> Edit on GitHub</a>
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diff --git a/development/how-to-run/index.html b/development/how-to-run/index.html
@@ -98,7 +98,7 @@
     <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/d71ba5e0e8ef346522695b8431a324a67acf0fab/README.md" class="icon icon-github"> Edit on GitHub</a>
+          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/1d736cdbe898a786b20b3b494d215c1a563a7574/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/d71ba5e0e8ef346522695b8431a324a67acf0fab/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/1d736cdbe898a786b20b3b494d215c1a563a7574/config/template.config">Example config</a>).</p>
 </li>
 <li>
-<p>Update the YAML (<a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/d71ba5e0e8ef346522695b8431a324a67acf0fab/input">Template YAMLs</a>).</p>
+<p>Update the YAML (<a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/1d736cdbe898a786b20b3b494d215c1a563a7574/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>

diff --git a/development/index.html b/development/index.html
@@ -98,7 +98,7 @@
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+          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/1d736cdbe898a786b20b3b494d215c1a563a7574/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>
 
 <!--
 MkDocs version : 1.5.3
-Build Date UTC : 2024-05-06 22:04:41.618072+00:00
+Build Date UTC : 2024-05-17 16:57:17.060401+00:00
 -->
diff --git a/development/inputs/index.html b/development/inputs/index.html
@@ -106,7 +106,7 @@
     <li><a href=".." class="icon icon-home" aria-label="Docs"></a></li>
       <li class="breadcrumb-item active">Inputs</li>
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-          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/d71ba5e0e8ef346522695b8431a324a67acf0fab/README.md" class="icon icon-github"> Edit on GitHub</a>
+          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/1d736cdbe898a786b20b3b494d215c1a563a7574/README.md" class="icon icon-github"> Edit on GitHub</a>
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@@ -327,7 +327,7 @@ <h3 id="config">Config</h3>
 </tbody>
 </table>
 <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/d71ba5e0e8ef346522695b8431a324a67acf0fab/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/1d736cdbe898a786b20b3b494d215c1a563a7574/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;],

diff --git a/development/license/index.html b/development/license/index.html
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+          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/1d736cdbe898a786b20b3b494d215c1a563a7574/README.md" class="icon icon-github"> Edit on GitHub</a>
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diff --git a/development/outputs/index.html b/development/outputs/index.html
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       <li class="breadcrumb-item active">Outputs</li>
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+          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/1d736cdbe898a786b20b3b494d215c1a563a7574/README.md" class="icon icon-github"> Edit on GitHub</a>
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diff --git a/development/overview/index.html b/development/overview/index.html
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       <li class="breadcrumb-item active">Overview</li>
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+          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/1d736cdbe898a786b20b3b494d215c1a563a7574/README.md" class="icon icon-github"> Edit on GitHub</a>
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diff --git a/development/pipeline-steps/index.html b/development/pipeline-steps/index.html
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+          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/1d736cdbe898a786b20b3b494d215c1a563a7574/README.md" class="icon icon-github"> Edit on GitHub</a>
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diff --git a/development/references/index.html b/development/references/index.html
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+          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/1d736cdbe898a786b20b3b494d215c1a563a7574/README.md" class="icon icon-github"> Edit on GitHub</a>
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diff --git a/development/sitemap.xml.gz b/development/sitemap.xml.gz
diff --git a/versions.json b/versions.json
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     "aliases": [],
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-      "commit": "d71ba5e0e8ef346522695b8431a324a67acf0fab",
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+      "date": "2024-05-17T09:56:42-07:00"
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