Deployed d40c8b0 to development with MkDocs 1.5.3 and mike 2.0.0

uclahs-cds · Oct 25, 2024 · 43a493d · 43a493d
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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>
     <li class="wy-breadcrumbs-aside">
-          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/7aaae3466345f0287d1cb5980a268d55dac24ec1/README.md" class="icon icon-github"> Edit on GitHub</a>
+          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/d40c8b0316fb2c30dd1cba37dc09eee0fbce782c/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 @@
     <li><a href=".." class="icon icon-home" aria-label="Docs"></a></li>
       <li class="breadcrumb-item active">Discussions</li>
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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>
+          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/d40c8b0316fb2c30dd1cba37dc09eee0fbce782c/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
@@ -98,7 +98,7 @@
     <li><a href=".." class="icon icon-home" aria-label="Docs"></a></li>
       <li class="breadcrumb-item active">Flow Diagram</li>
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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>
+          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/d40c8b0316fb2c30dd1cba37dc09eee0fbce782c/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>
     <li class="wy-breadcrumbs-aside">
-          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/7aaae3466345f0287d1cb5980a268d55dac24ec1/README.md" class="icon icon-github"> Edit on GitHub</a>
+          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/d40c8b0316fb2c30dd1cba37dc09eee0fbce782c/README.md" class="icon icon-github"> Edit on GitHub</a>
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   <hr/>
@@ -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/7aaae3466345f0287d1cb5980a268d55dac24ec1/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/d40c8b0316fb2c30dd1cba37dc09eee0fbce782c/config/template.config">Example config</a>).</p>
 </li>
 <li>
-<p>Update the YAML (<a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/7aaae3466345f0287d1cb5980a268d55dac24ec1/input">Template YAMLs</a>).</p>
+<p>Update the YAML (<a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/d40c8b0316fb2c30dd1cba37dc09eee0fbce782c/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 @@
     <li><a href="." class="icon icon-home" aria-label="Docs"></a></li>
       <li class="breadcrumb-item active">Home</li>
     <li class="wy-breadcrumbs-aside">
-          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/7aaae3466345f0287d1cb5980a268d55dac24ec1/README.md" class="icon icon-github"> Edit on GitHub</a>
+          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/d40c8b0316fb2c30dd1cba37dc09eee0fbce782c/README.md" class="icon icon-github"> Edit on GitHub</a>
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   <hr/>
@@ -170,5 +170,5 @@ <h1 id="recalibrate-bam">recalibrate-BAM</h1>
 
 <!--
 MkDocs version : 1.5.3
-Build Date UTC : 2024-10-09 00:13:59.773947+00:00
+Build Date UTC : 2024-10-25 23:46:12.261120+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>
     <li class="wy-breadcrumbs-aside">
-          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/7aaae3466345f0287d1cb5980a268d55dac24ec1/README.md" class="icon icon-github"> Edit on GitHub</a>
+          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/d40c8b0316fb2c30dd1cba37dc09eee0fbce782c/README.md" class="icon icon-github"> Edit on GitHub</a>
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   <hr/>
@@ -262,31 +262,31 @@ <h3 id="config">Config</h3>
 <td style="text-align: left;"><code>reference_fasta</code></td>
 <td style="text-align: left;">Yes</td>
 <td style="text-align: left;">path</td>
-<td style="text-align: left;">Absolute path to reference genome fasta file, e.g., <code>/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta</code></td>
+<td style="text-align: left;">Absolute path to reference genome fasta file, e.g., <code>/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta</code></td>
 </tr>
 <tr>
 <td style="text-align: left;"><code>bundle_mills_and_1000g_gold_standard_indels_vcf_gz</code></td>
 <td style="text-align: left;">Yes</td>
 <td style="text-align: left;">path</td>
-<td style="text-align: left;">Absolute path to Mills &amp; 1000G Gold Standard Indels file, e.g., <code>/hot/ref/tool-specific-input/GATK/GRCh38/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz</code></td>
+<td style="text-align: left;">Absolute path to Mills &amp; 1000G Gold Standard Indels file, e.g., <code>/hot/resource/tool-specific-input/GATK/GRCh38/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz</code></td>
 </tr>
 <tr>
 <td style="text-align: left;"><code>bundle_known_indels_vcf_gz</code></td>
 <td style="text-align: left;">Yes</td>
 <td style="text-align: left;">path</td>
-<td style="text-align: left;">Absolute path to known indels file, e.g., <code>/hot/ref/tool-specific-input/GATK/GRCh38/Homo_sapiens_assembly38.known_indels.vcf.gz</code></td>
+<td style="text-align: left;">Absolute path to known indels file, e.g., <code>/hot/resource/tool-specific-input/GATK/GRCh38/Homo_sapiens_assembly38.known_indels.vcf.gz</code></td>
 </tr>
 <tr>
 <td style="text-align: left;"><code>bundle_v0_dbsnp138_vcf_gz</code></td>
 <td style="text-align: left;">Yes</td>
 <td style="text-align: left;">path</td>
-<td style="text-align: left;">Absolute path to dbsnp file, e.g., <code>/hot/ref/tool-specific-input/GATK/GRCh38/resources_broad_hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf.gz</code></td>
+<td style="text-align: left;">Absolute path to dbsnp file, e.g., <code>/hot/resource/tool-specific-input/GATK/GRCh38/resources_broad_hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf.gz</code></td>
 </tr>
 <tr>
 <td style="text-align: left;"><code>bundle_contest_hapmap_3p3_vcf_gz</code></td>
 <td style="text-align: left;">Yes</td>
 <td style="text-align: left;">path</td>
-<td style="text-align: left;">Absolute path to HapMap 3.3 biallelic sites file, e.g., <code>/hot/ref/tool-specific-input/GATK/GRCh38/Biallelic/hapmap_3.3.hg38.BIALLELIC.PASS.2021-09-01.vcf.gz</code></td>
+<td style="text-align: left;">Absolute path to HapMap 3.3 biallelic sites file, e.g., <code>/hot/resource/tool-specific-input/GATK/GRCh38/Biallelic/hapmap_3.3.hg38.BIALLELIC.PASS.2021-09-01.vcf.gz</code></td>
 </tr>
 <tr>
 <td style="text-align: left;"><code>work_dir</code></td>
@@ -302,7 +302,7 @@ <h3 id="config">Config</h3>
 </tr>
 </tbody>
 </table>
-<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>
+<p>The below parameters have default values defined in <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/d40c8b0316fb2c30dd1cba37dc09eee0fbce782c/config/default.config"><code>default.config</code></a> and generally do not need to be set by the user.</p>
 <table>
 <thead>
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@@ -395,7 +395,7 @@ <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/7aaae3466345f0287d1cb5980a268d55dac24ec1/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/d40c8b0316fb2c30dd1cba37dc09eee0fbce782c/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
@@ -98,7 +98,7 @@
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       <li class="breadcrumb-item active">License</li>
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+          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/d40c8b0316fb2c30dd1cba37dc09eee0fbce782c/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
@@ -98,7 +98,7 @@
     <li><a href=".." class="icon icon-home" aria-label="Docs"></a></li>
       <li class="breadcrumb-item active">Outputs</li>
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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>
+          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/d40c8b0316fb2c30dd1cba37dc09eee0fbce782c/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
@@ -98,7 +98,7 @@
     <li><a href=".." class="icon icon-home" aria-label="Docs"></a></li>
       <li class="breadcrumb-item active">Overview</li>
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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>
+          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/d40c8b0316fb2c30dd1cba37dc09eee0fbce782c/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
@@ -122,7 +122,7 @@
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       <li class="breadcrumb-item active">Pipeline Steps</li>
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+          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/d40c8b0316fb2c30dd1cba37dc09eee0fbce782c/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
@@ -98,7 +98,7 @@
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       <li class="breadcrumb-item active">References</li>
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+          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/d40c8b0316fb2c30dd1cba37dc09eee0fbce782c/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
@@ -4,16 +4,16 @@
     "title": "development",
     "aliases": [],
     "properties": {
-      "commit": "7aaae3466345f0287d1cb5980a268d55dac24ec1",
-      "date": "2024-10-08T17:12:38-07:00"
+      "commit": "d40c8b0316fb2c30dd1cba37dc09eee0fbce782c",
+      "date": "2024-10-25T16:45:37-07:00"
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   },
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     "version": "v1.0.2",
     "title": "v1.0.2",
     "aliases": [
-      "latest",
-      "release-candidate"
+      "release-candidate",
+      "latest"
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     "properties": {
       "commit": "7aaae3466345f0287d1cb5980a268d55dac24ec1",