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development/flow-diagrams---variant-calling/index.html

@@ -106,7 +106,7 @@
     <li><a href=".." class="icon icon-home" aria-label="Docs"></a></li>
       <li class="breadcrumb-item active">Flow Diagrams - Variant Calling</li>
     <li class="wy-breadcrumbs-aside">
-          <a href="https://github.com/uclahs-cds/pipeline-call-sSNV/blob/e061aa52d59d6bedc064d20b72cbffc2f40ee341/README.md" class="icon icon-github"> Edit on GitHub</a>
+          <a href="https://github.com/uclahs-cds/pipeline-call-sSNV/blob/e038942c61a8bee4c311efb1ad991c0ecac45845/README.md" class="icon icon-github"> Edit on GitHub</a>
     </li>
   </ul>
   <hr/>

development/flow-diagrams---variant-intersection/index.html

@@ -100,7 +100,7 @@
     <li><a href=".." class="icon icon-home" aria-label="Docs"></a></li>
       <li class="breadcrumb-item active">Flow Diagrams - Variant Intersection</li>
     <li class="wy-breadcrumbs-aside">
-          <a href="https://github.com/uclahs-cds/pipeline-call-sSNV/blob/e061aa52d59d6bedc064d20b72cbffc2f40ee341/README.md" class="icon icon-github"> Edit on GitHub</a>
+          <a href="https://github.com/uclahs-cds/pipeline-call-sSNV/blob/e038942c61a8bee4c311efb1ad991c0ecac45845/README.md" class="icon icon-github"> Edit on GitHub</a>
     </li>
   </ul>
   <hr/>

development/flowcharts/index.html

@@ -96,7 +96,7 @@
     <li><a href=".." class="icon icon-home" aria-label="Docs"></a></li>
       <li class="breadcrumb-item active">pipeline-call-sSNV Flow Diagrams and Tool Links</li>
     <li class="wy-breadcrumbs-aside">
-          <a href="https://github.com/uclahs-cds/pipeline-call-sSNV/blob/e061aa52d59d6bedc064d20b72cbffc2f40ee341/README.md" class="icon icon-github"> Edit on GitHub</a>
+          <a href="https://github.com/uclahs-cds/pipeline-call-sSNV/blob/e038942c61a8bee4c311efb1ad991c0ecac45845/README.md" class="icon icon-github"> Edit on GitHub</a>
     </li>
   </ul>
   <hr/>

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-call-sSNV/blob/e061aa52d59d6bedc064d20b72cbffc2f40ee341/README.md" class="icon icon-github"> Edit on GitHub</a>
+          <a href="https://github.com/uclahs-cds/pipeline-call-sSNV/blob/e038942c61a8bee4c311efb1ad991c0ecac45845/README.md" class="icon icon-github"> Edit on GitHub</a>
     </li>
   </ul>
   <hr/>
@@ -119,23 +119,23 @@ <h2 id="how-to-run">How To Run</h2>
 <p>The source code should never be modified when running our pipelines</p>
 </li>
 <li>
-<p>Copy and edit the <a href="https://github.com/uclahs-cds/pipeline-call-sSNV/blob/e061aa52d59d6bedc064d20b72cbffc2f40ee341/config/template.config">input config file</a></p>
+<p>Copy and edit the <a href="https://github.com/uclahs-cds/pipeline-call-sSNV/blob/e038942c61a8bee4c311efb1ad991c0ecac45845/config/template.config">input config file</a></p>
 </li>
 </ol>
 <blockquote>
 <p>Make sure the reference .fa file in config file matches the reference genome in the input BAM files.</p>
 </blockquote>
 <ol>
-<li>Copy and edit the <a href="https://github.com/uclahs-cds/pipeline-call-sSNV/blob/e061aa52d59d6bedc064d20b72cbffc2f40ee341/input/call-sSNV-template.yaml">input YAML</a></li>
+<li>Copy and edit the <a href="https://github.com/uclahs-cds/pipeline-call-sSNV/blob/e038942c61a8bee4c311efb1ad991c0ecac45845/input/call-sSNV-template.yaml">input YAML</a></li>
 <li>The pipeline can be executed locally using the command below:</li>
 </ol>
 <pre><code class="language-bash">nextflow run path/to/main.nf -config path/to/input.config -params-file input.yaml`
 </code></pre>
 <p>For example,</p>
 <ul>
 <li><code>path/to/main.nf</code> could be: <code>/hot/software/pipeline/pipeline-call-sSNV/Nextflow/release/5.0.0/main.nf</code></li>
-<li><code>path/to/input.config</code> is the path to where you saved your project-specific copy of <a href="https://github.com/uclahs-cds/pipeline-call-sSNV/blob/e061aa52d59d6bedc064d20b72cbffc2f40ee341/config/template.config">template.config</a></li>
-<li><code>path/to/input.yaml</code> is the path to where you saved your project-specific copy of <a href="https://github.com/uclahs-cds/pipeline-call-sSNV/blob/e061aa52d59d6bedc064d20b72cbffc2f40ee341/input/call-sSNV-template.yaml">template.yaml</a></li>
+<li><code>path/to/input.config</code> is the path to where you saved your project-specific copy of <a href="https://github.com/uclahs-cds/pipeline-call-sSNV/blob/e038942c61a8bee4c311efb1ad991c0ecac45845/config/template.config">template.config</a></li>
+<li><code>path/to/input.yaml</code> is the path to where you saved your project-specific copy of <a href="https://github.com/uclahs-cds/pipeline-call-sSNV/blob/e038942c61a8bee4c311efb1ad991c0ecac45845/input/call-sSNV-template.yaml">template.yaml</a></li>
 </ul>
 <p>To submit to UCLAHS-CDS's Azure cloud, use the submission script <a href="https://github.com/uclahs-cds/tool-submit-nf">here</a> with the command below:</p>
 <pre><code class="language-bash">python path/to/submit_nextflow_pipeline.py \

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-call-sSNV/blob/e061aa52d59d6bedc064d20b72cbffc2f40ee341/README.md" class="icon icon-github"> Edit on GitHub</a>
+          <a href="https://github.com/uclahs-cds/pipeline-call-sSNV/blob/e038942c61a8bee4c311efb1ad991c0ecac45845/README.md" class="icon icon-github"> Edit on GitHub</a>
     </li>
   </ul>
   <hr/>
@@ -187,5 +187,5 @@ <h1 id="pipeline-call-ssnv">pipeline-call-sSNV</h1>
 
 <!--
 MkDocs version : 1.5.3
-Build Date UTC : 2024-05-13 22:49:10.906634+00:00
+Build Date UTC : 2024-05-15 17:31:00.237879+00:00
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development/inputs/index.html

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     <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-call-sSNV/blob/e061aa52d59d6bedc064d20b72cbffc2f40ee341/README.md" class="icon icon-github"> Edit on GitHub</a>
+          <a href="https://github.com/uclahs-cds/pipeline-call-sSNV/blob/e038942c61a8bee4c311efb1ad991c0ecac45845/README.md" class="icon icon-github"> Edit on GitHub</a>
     </li>
   </ul>
   <hr/>
@@ -124,7 +124,7 @@
 
                 <h2 id="inputs">Inputs</h2>
 <p>To run the pipeline, one <code>input.yaml</code> and one <code>input.config</code> are needed, as follows.</p>
-<h3 id="inputyaml-see-template">input.yaml. (<a href="https://github.com/uclahs-cds/pipeline-call-sSNV/blob/e061aa52d59d6bedc064d20b72cbffc2f40ee341/input/call-sSNV-template.yaml">see template</a>)</h3>
+<h3 id="inputyaml-see-template">input.yaml. (<a href="https://github.com/uclahs-cds/pipeline-call-sSNV/blob/e038942c61a8bee4c311efb1ad991c0ecac45845/input/call-sSNV-template.yaml">see template</a>)</h3>
 <table>
 <thead>
 <tr>
@@ -168,9 +168,9 @@ <h3 id="inputyaml-see-template">input.yaml. (<a href="https://github.com/uclahs-
       contamination_table: /path/to/contamination.table
 </code></pre>
 <ul>
-<li><code>Mutect2</code> can take other inputs: tumor-only sample and one patient's multiple samples. For tumor-only samples, remove the normal input in <code>input.yaml</code>, e.g. <a href="https://github.com/uclahs-cds/pipeline-call-sSNV/blob/e061aa52d59d6bedc064d20b72cbffc2f40ee341/input/example-test-tumor-only.yaml">template_tumor_only.yaml</a>. For multiple samples, put all the input BAMs in the <code>input.yaml</code>, e.g. <a href="https://github.com/uclahs-cds/pipeline-call-sSNV/blob/e061aa52d59d6bedc064d20b72cbffc2f40ee341/input/example-test-multi-sample.yaml">template_multi_sample.yaml</a>. Note, for these non-standard inputs, the configuration file must have 'mutect2' listed as the only algorithm.</li>
+<li><code>Mutect2</code> can take other inputs: tumor-only sample and one patient's multiple samples. For tumor-only samples, remove the normal input in <code>input.yaml</code>, e.g. <a href="https://github.com/uclahs-cds/pipeline-call-sSNV/blob/e038942c61a8bee4c311efb1ad991c0ecac45845/input/example-test-tumor-only.yaml">template_tumor_only.yaml</a>. For multiple samples, put all the input BAMs in the <code>input.yaml</code>, e.g. <a href="https://github.com/uclahs-cds/pipeline-call-sSNV/blob/e038942c61a8bee4c311efb1ad991c0ecac45845/input/example-test-multi-sample.yaml">template_multi_sample.yaml</a>. Note, for these non-standard inputs, the configuration file must have 'mutect2' listed as the only algorithm.</li>
 </ul>
-<h3 id="inputconfig-see-template">input.config (<a href="https://github.com/uclahs-cds/pipeline-call-sSNV/blob/e061aa52d59d6bedc064d20b72cbffc2f40ee341/config/template.config">see template</a>)</h3>
+<h3 id="inputconfig-see-template">input.config (<a href="https://github.com/uclahs-cds/pipeline-call-sSNV/blob/e038942c61a8bee4c311efb1ad991c0ecac45845/config/template.config">see template</a>)</h3>
 <table>
 <thead>
 <tr>
@@ -245,7 +245,7 @@ <h3 id="inputconfig-see-template">input.config (<a href="https://github.com/ucla
 </table>
 <p>*Providing <code>intersect_regions</code> is required and will limit the final output to just those regions.  All regions of the reference genome could be provided as a <code>bed</code> file with all contigs, however it is HIGHLY recommended to remove <code>decoy</code> contigs from the human reference genome. Including these thousands of small contigs will require the user to increase available memory for <code>Mutect2</code> and will cause a very long runtime for <code>Strelka2</code>. See <a href="https://github.com/uclahs-cds/pipeline-call-sSNV/discussions/216">Discussion here</a>. For <code>uclahs-cds</code> users, a GRCh38 <code>bed.gz</code> file can be found here: <code>/hot/ref/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz</code>.</p>
 <h3 id="base-resource-allocation-updaters">Base resource allocation updaters</h3>
-<p>To optionally update the base resource (cpus or memory) allocations for processes, use the following structure and add the necessary parts to the <a href="https://github.com/uclahs-cds/pipeline-call-sSNV/blob/e061aa52d59d6bedc064d20b72cbffc2f40ee341/config/template.config">input.config</a> file. The default allocations can be found in the <a href="https://github.com/uclahs-cds/pipeline-call-sSNV/blob/e061aa52d59d6bedc064d20b72cbffc2f40ee341/config">node-specific config files</a></p>
+<p>To optionally update the base resource (cpus or memory) allocations for processes, use the following structure and add the necessary parts to the <a href="https://github.com/uclahs-cds/pipeline-call-sSNV/blob/e038942c61a8bee4c311efb1ad991c0ecac45845/config/template.config">input.config</a> file. The default allocations can be found in the <a href="https://github.com/uclahs-cds/pipeline-call-sSNV/blob/e038942c61a8bee4c311efb1ad991c0ecac45845/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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     <li><a href=".." class="icon icon-home" aria-label="Docs"></a></li>
       <li class="breadcrumb-item active">License</li>
     <li class="wy-breadcrumbs-aside">
-          <a href="https://github.com/uclahs-cds/pipeline-call-sSNV/blob/e061aa52d59d6bedc064d20b72cbffc2f40ee341/README.md" class="icon icon-github"> Edit on GitHub</a>
+          <a href="https://github.com/uclahs-cds/pipeline-call-sSNV/blob/e038942c61a8bee4c311efb1ad991c0ecac45845/README.md" class="icon icon-github"> Edit on GitHub</a>
     </li>
   </ul>
   <hr/>

development/outputs/index.html

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     <li><a href=".." class="icon icon-home" aria-label="Docs"></a></li>
       <li class="breadcrumb-item active">Outputs</li>
     <li class="wy-breadcrumbs-aside">
-          <a href="https://github.com/uclahs-cds/pipeline-call-sSNV/blob/e061aa52d59d6bedc064d20b72cbffc2f40ee341/README.md" class="icon icon-github"> Edit on GitHub</a>
+          <a href="https://github.com/uclahs-cds/pipeline-call-sSNV/blob/e038942c61a8bee4c311efb1ad991c0ecac45845/README.md" class="icon icon-github"> Edit on GitHub</a>
     </li>
   </ul>
   <hr/>

development/overview/index.html

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     <li><a href=".." class="icon icon-home" aria-label="Docs"></a></li>
       <li class="breadcrumb-item active">Overview</li>
     <li class="wy-breadcrumbs-aside">
-          <a href="https://github.com/uclahs-cds/pipeline-call-sSNV/blob/e061aa52d59d6bedc064d20b72cbffc2f40ee341/README.md" class="icon icon-github"> Edit on GitHub</a>
+          <a href="https://github.com/uclahs-cds/pipeline-call-sSNV/blob/e038942c61a8bee4c311efb1ad991c0ecac45845/README.md" class="icon icon-github"> Edit on GitHub</a>
     </li>
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development/pipeline-steps---variant-calling/index.html

@@ -152,7 +152,7 @@
     <li><a href=".." class="icon icon-home" aria-label="Docs"></a></li>
       <li class="breadcrumb-item active">Pipeline Steps - Variant Calling</li>
     <li class="wy-breadcrumbs-aside">
-          <a href="https://github.com/uclahs-cds/pipeline-call-sSNV/blob/e061aa52d59d6bedc064d20b72cbffc2f40ee341/README.md" class="icon icon-github"> Edit on GitHub</a>
+          <a href="https://github.com/uclahs-cds/pipeline-call-sSNV/blob/e038942c61a8bee4c311efb1ad991c0ecac45845/README.md" class="icon icon-github"> Edit on GitHub</a>
     </li>
   </ul>
   <hr/>

development/pipeline-steps---variant-intersection/index.html

@@ -106,7 +106,7 @@
     <li><a href=".." class="icon icon-home" aria-label="Docs"></a></li>
       <li class="breadcrumb-item active">Pipeline Steps - Variant Intersection</li>
     <li class="wy-breadcrumbs-aside">
-          <a href="https://github.com/uclahs-cds/pipeline-call-sSNV/blob/e061aa52d59d6bedc064d20b72cbffc2f40ee341/README.md" class="icon icon-github"> Edit on GitHub</a>
+          <a href="https://github.com/uclahs-cds/pipeline-call-sSNV/blob/e038942c61a8bee4c311efb1ad991c0ecac45845/README.md" class="icon icon-github"> Edit on GitHub</a>
     </li>
   </ul>
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development/references/index.html

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     <li><a href=".." class="icon icon-home" aria-label="Docs"></a></li>
       <li class="breadcrumb-item active">References</li>
     <li class="wy-breadcrumbs-aside">
-          <a href="https://github.com/uclahs-cds/pipeline-call-sSNV/blob/e061aa52d59d6bedc064d20b72cbffc2f40ee341/README.md" class="icon icon-github"> Edit on GitHub</a>
+          <a href="https://github.com/uclahs-cds/pipeline-call-sSNV/blob/e038942c61a8bee4c311efb1ad991c0ecac45845/README.md" class="icon icon-github"> Edit on GitHub</a>
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versions.json

@@ -4,16 +4,16 @@
     "title": "development",
     "aliases": [],
     "properties": {
-      "commit": "e061aa52d59d6bedc064d20b72cbffc2f40ee341",
-      "date": "2024-05-13T15:48:24-07:00"
+      "commit": "e038942c61a8bee4c311efb1ad991c0ecac45845",
+      "date": "2024-05-15T10:29:46-07:00"
     }
   },
   {
     "version": "v8.0.0",
     "title": "v8.0.0",
     "aliases": [
-      "release-candidate",
-      "latest"
+      "latest",
+      "release-candidate"
     ],
     "properties": {
       "commit": "c7baf125497fe5c051678e3463fbb29fb92bf3e6",