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uclahs-cds · Apr 10, 2024 · 215be45 · 215be45
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diff --git a/development/call-gsnp-flow.puml b/development/call-gsnp-flow.puml
@@ -0,0 +1,87 @@
+@startuml
+
+skinparam ConditionEndStyle hline
+
+start
+
+if (Explicit intervals?) is (Yes) then
+    :==run_SplitIntervals_GATK
+    ----
+    Split reference genome into up
+    to **scatter_count** interval lists,
+    without subdividing any of the
+    input intervals;
+else (No)
+    :==run_SplitIntervals_GATK
+    ----
+    Split reference genome into
+    **scatter_count** interval lists;
+endif
+
+split
+
+:==run_HaplotypeCallerVCF_GATK
+----
+Generate VCFs for each split interval
+using HaplotypeCaller;
+
+:==run_MergeVcfs_Picard_VCF
+----
+Merge raw variants into whole VCF file;
+
+#palegreen:Per-sample raw VCF + index files>
+
+partition "Recalibrate Variants" {
+
+:==run_VariantRecalibratorSNP_GATK
+----
+Generate Variant Quality Score Recalibration
+(VQSR) table for SNPs;
+
+:==run_ApplyVQSR_GATK_SNP
+----
+Filter SNPs based on VQSR table;
+
+:==run_VariantRecalibratorINDEL_GATK
+----
+Generate VQSR table for INDELs;
+
+:==run_ApplyVQSR_GATK_INDEL
+----
+Filter INDELs based on VQSR table;
+
+}
+
+#palegreen:SNP and INDEL recalibrated
+variants + index files>
+
+:==filter_gSNP_GATK
+----
+Filter ambiguous variants with
+customized Perl script;
+
+#palegreen:Filtered germline
+variants + index files>
+
+detach
+
+split again
+
+:==run_HaplotypeCallerGVCF_GATK
+----
+Generate GVCFs for each split interval
+using HaplotypeCaller;
+
+:==run_MergeVcfs_Picard_GVCF
+----
+Merge raw variants into whole GVCF file;
+
+#palegreen:Per-sample GVCF + index files>
+
+detach
+
+endsplit
+
+
+@enduml
+
diff --git a/development/call-gsnp-flow.svg b/development/call-gsnp-flow.svg
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-call-gSNP/blob/48e4521e02d727dada5586043afe00680906eef8/README.md" class="icon icon-github"> Edit on GitHub</a>
+          <a href="https://github.com/uclahs-cds/pipeline-call-gSNP/blob/f42b9ae9776e8be97e50e72f1f56d6b16373697d/README.md" class="icon icon-github"> Edit on GitHub</a>
     </li>
   </ul>
   <hr/>

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>
     <li class="wy-breadcrumbs-aside">
-          <a href="https://github.com/uclahs-cds/pipeline-call-gSNP/blob/48e4521e02d727dada5586043afe00680906eef8/README.md" class="icon icon-github"> Edit on GitHub</a>
+          <a href="https://github.com/uclahs-cds/pipeline-call-gSNP/blob/f42b9ae9776e8be97e50e72f1f56d6b16373697d/README.md" class="icon icon-github"> Edit on GitHub</a>
     </li>
   </ul>
   <hr/>

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>
     <li class="wy-breadcrumbs-aside">
-          <a href="https://github.com/uclahs-cds/pipeline-call-gSNP/blob/48e4521e02d727dada5586043afe00680906eef8/README.md" class="icon icon-github"> Edit on GitHub</a>
+          <a href="https://github.com/uclahs-cds/pipeline-call-gSNP/blob/f42b9ae9776e8be97e50e72f1f56d6b16373697d/README.md" class="icon icon-github"> Edit on GitHub</a>
     </li>
   </ul>
   <hr/>
@@ -107,7 +107,7 @@
             <div class="section" itemprop="articleBody">
 
                 <h2 id="flow-diagram">Flow Diagram</h2>
-<p><img alt="call-gSNP flow diagram" src="../img/call-gSNP-DSL2.png" /></p>
+<p><img alt="call-gSNP flow diagram" src="../call-gsnp-flow.svg" /></p>
 <hr />
 
             </div>

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-call-gSNP/blob/48e4521e02d727dada5586043afe00680906eef8/README.md" class="icon icon-github"> Edit on GitHub</a>
+          <a href="https://github.com/uclahs-cds/pipeline-call-gSNP/blob/f42b9ae9776e8be97e50e72f1f56d6b16373697d/README.md" class="icon icon-github"> Edit on GitHub</a>
     </li>
   </ul>
   <hr/>
@@ -110,7 +110,7 @@ <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-call-gSNP/blob/48e4521e02d727dada5586043afe00680906eef8/config/template.config">Example config</a>).</p>
+<p>Update the params section of the .config file (<a href="https://github.com/uclahs-cds/pipeline-call-gSNP/blob/f42b9ae9776e8be97e50e72f1f56d6b16373697d/config/template.config">Example config</a>).</p>
 </li>
 <li>
 <p>Update the YAML.</p>

diff --git a/development/img/call-gSNP-DSL2.png b/development/img/call-gSNP-DSL2.png
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-call-gSNP/blob/48e4521e02d727dada5586043afe00680906eef8/README.md" class="icon icon-github"> Edit on GitHub</a>
+          <a href="https://github.com/uclahs-cds/pipeline-call-gSNP/blob/f42b9ae9776e8be97e50e72f1f56d6b16373697d/README.md" class="icon icon-github"> Edit on GitHub</a>
     </li>
   </ul>
   <hr/>
@@ -170,5 +170,5 @@ <h1 id="call-gsnp">call-gSNP</h1>
 
 <!--
 MkDocs version : 1.5.3
-Build Date UTC : 2024-03-09 01:12:42.811091+00:00
+Build Date UTC : 2024-04-10 16:25:11.521664+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-call-gSNP/blob/48e4521e02d727dada5586043afe00680906eef8/README.md" class="icon icon-github"> Edit on GitHub</a>
+          <a href="https://github.com/uclahs-cds/pipeline-call-gSNP/blob/f42b9ae9776e8be97e50e72f1f56d6b16373697d/README.md" class="icon icon-github"> Edit on GitHub</a>
     </li>
   </ul>
   <hr/>
@@ -265,7 +265,7 @@ <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-call-gSNP/blob/48e4521e02d727dada5586043afe00680906eef8/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-call-gSNP/blob/f42b9ae9776e8be97e50e72f1f56d6b16373697d/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 @@
     <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-gSNP/blob/48e4521e02d727dada5586043afe00680906eef8/README.md" class="icon icon-github"> Edit on GitHub</a>
+          <a href="https://github.com/uclahs-cds/pipeline-call-gSNP/blob/f42b9ae9776e8be97e50e72f1f56d6b16373697d/README.md" class="icon icon-github"> Edit on GitHub</a>
     </li>
   </ul>
   <hr/>

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>
     <li class="wy-breadcrumbs-aside">
-          <a href="https://github.com/uclahs-cds/pipeline-call-gSNP/blob/48e4521e02d727dada5586043afe00680906eef8/README.md" class="icon icon-github"> Edit on GitHub</a>
+          <a href="https://github.com/uclahs-cds/pipeline-call-gSNP/blob/f42b9ae9776e8be97e50e72f1f56d6b16373697d/README.md" class="icon icon-github"> Edit on GitHub</a>
     </li>
   </ul>
   <hr/>

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>
     <li class="wy-breadcrumbs-aside">
-          <a href="https://github.com/uclahs-cds/pipeline-call-gSNP/blob/48e4521e02d727dada5586043afe00680906eef8/README.md" class="icon icon-github"> Edit on GitHub</a>
+          <a href="https://github.com/uclahs-cds/pipeline-call-gSNP/blob/f42b9ae9776e8be97e50e72f1f56d6b16373697d/README.md" class="icon icon-github"> Edit on GitHub</a>
     </li>
   </ul>
   <hr/>

diff --git a/development/pipeline-steps/index.html b/development/pipeline-steps/index.html
@@ -57,7 +57,7 @@
     <ul class="current">
     <li class="toctree-l2"><a class="reference internal" href="#1-split-genome-or-target-intervals-into-sub-intervals-for-parallelization">1. Split genome or target intervals into sub-intervals for parallelization</a>
     </li>
-    <li class="toctree-l2"><a class="reference internal" href="#2-haplotypecaller">2.  HaplotypeCaller</a>
+    <li class="toctree-l2"><a class="reference internal" href="#2-haplotypecaller">2. HaplotypeCaller</a>
     </li>
     <li class="toctree-l2"><a class="reference internal" href="#3-merge-raw-vcfs-and-gvcfs">3. Merge raw VCFs and GVCFs</a>
     </li>
@@ -120,7 +120,7 @@
     <li><a href=".." class="icon icon-home" aria-label="Docs"></a></li>
       <li class="breadcrumb-item active">Pipeline Steps</li>
     <li class="wy-breadcrumbs-aside">
-          <a href="https://github.com/uclahs-cds/pipeline-call-gSNP/blob/48e4521e02d727dada5586043afe00680906eef8/README.md" class="icon icon-github"> Edit on GitHub</a>
+          <a href="https://github.com/uclahs-cds/pipeline-call-gSNP/blob/f42b9ae9776e8be97e50e72f1f56d6b16373697d/README.md" class="icon icon-github"> Edit on GitHub</a>
     </li>
   </ul>
   <hr/>

diff --git a/development/references/index.html b/development/references/index.html
@@ -98,7 +98,7 @@
     <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-gSNP/blob/48e4521e02d727dada5586043afe00680906eef8/README.md" class="icon icon-github"> Edit on GitHub</a>
+          <a href="https://github.com/uclahs-cds/pipeline-call-gSNP/blob/f42b9ae9776e8be97e50e72f1f56d6b16373697d/README.md" class="icon icon-github"> Edit on GitHub</a>
     </li>
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   <hr/>

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": "48e4521e02d727dada5586043afe00680906eef8",
-      "date": "2024-03-08T17:11:15-08:00"
+      "commit": "f42b9ae9776e8be97e50e72f1f56d6b16373697d",
+      "date": "2024-04-10T09:24:25-07:00"
     }
   },
   {
     "version": "v10.0.0",
     "title": "v10.0.0",
     "aliases": [
-      "release-candidate",
-      "latest"
+      "latest",
+      "release-candidate"
     ],
     "properties": {
       "commit": "48e4521e02d727dada5586043afe00680906eef8",