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uclahs-cds · May 7, 2024 · b0f78b7 · b0f78b7
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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-call-gSV/blob/1cf467fb660bb3cff75ed58c84187862fe61a690/README.md" class="icon icon-github"> Edit on GitHub</a>
+          <a href="https://github.com/uclahs-cds/pipeline-call-gSV/blob/43f8249ad83a310fdade2b36178cf4abac0c73f9/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-call-gSV/blob/43f8249ad83a310fdade2b36178cf4abac0c73f9/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
@@ -102,7 +102,7 @@
     <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-call-gSV/blob/1cf467fb660bb3cff75ed58c84187862fe61a690/README.md" class="icon icon-github"> Edit on GitHub</a>
+          <a href="https://github.com/uclahs-cds/pipeline-call-gSV/blob/43f8249ad83a310fdade2b36178cf4abac0c73f9/README.md" class="icon icon-github"> Edit on GitHub</a>
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@@ -124,13 +124,13 @@ <h3 id="run-steps">Run steps</h3>
 <p>The source code should never be modified when running our pipelines</p>
 </li>
 <li>
-<p>Create a config file for input, output, and parameters. An example for a config file can be found <a href="https://github.com/uclahs-cds/pipeline-call-gSV/blob/1cf467fb660bb3cff75ed58c84187862fe61a690/config/template.config">here</a>. See <a href="../inputs/#Nextflow-Config-File-Parameters">Nextflow Config File Parameters</a> for the detailed description of each variable in the config file.</p>
+<p>Create a config file for input, output, and parameters. An example for a config file can be found <a href="https://github.com/uclahs-cds/pipeline-call-gSV/blob/43f8249ad83a310fdade2b36178cf4abac0c73f9/config/template.config">here</a>. See <a href="../inputs/#Nextflow-Config-File-Parameters">Nextflow Config File Parameters</a> for the detailed description of each variable in the config file.</p>
 </li>
 <li>
 <p>Do not directly modify the source <code>template.config</code>, but rather you should copy it from the pipeline release folder to your project-specific folder and modify it there</p>
 </li>
 <li>
-<p>Create the input YAML using the <a href="https://github.com/uclahs-cds/pipeline-call-gSV/blob/1cf467fb660bb3cff75ed58c84187862fe61a690/input/call-gSV-input.yaml">template</a>. See <a href="../inputs/#Input-YAML">Input YAML</a> for a detailed description.</p>
+<p>Create the input YAML using the <a href="https://github.com/uclahs-cds/pipeline-call-gSV/blob/43f8249ad83a310fdade2b36178cf4abac0c73f9/input/call-gSV-input.yaml">template</a>. See <a href="../inputs/#Input-YAML">Input YAML</a> for a detailed description.</p>
 </li>
 <li>
 <p>Again, do not directly modify the source template YAML file.  Instead, copy it from the pipeline release folder to your project-specific folder and modify it there.</p>
@@ -143,8 +143,8 @@ <h3 id="run-steps">Run steps</h3>
 </code></pre>
 <ul>
 <li>For example, <code>path/to/main.nf</code> could be: <code>/hot/software/pipeline/pipeline-call-gSV/Nextflow/release/5.0.0-rc.1/main.nf</code></li>
-<li><code>path/to/sample-specific.config</code> is the path to where you saved your project-specific copy of <a href="https://github.com/uclahs-cds/pipeline-call-gSV/blob/1cf467fb660bb3cff75ed58c84187862fe61a690/config/template.config">template.config</a></li>
-<li><code>path/to/input.yaml</code> is the path to where you saved your sample-specific copy of <a href="https://github.com/uclahs-cds/pipeline-call-gSV/blob/1cf467fb660bb3cff75ed58c84187862fe61a690/input/call-gSV-input.yaml">call-gSV-input.yaml</a></li>
+<li><code>path/to/sample-specific.config</code> is the path to where you saved your project-specific copy of <a href="https://github.com/uclahs-cds/pipeline-call-gSV/blob/43f8249ad83a310fdade2b36178cf4abac0c73f9/config/template.config">template.config</a></li>
+<li><code>path/to/input.yaml</code> is the path to where you saved your sample-specific copy of <a href="https://github.com/uclahs-cds/pipeline-call-gSV/blob/43f8249ad83a310fdade2b36178cf4abac0c73f9/input/call-gSV-input.yaml">call-gSV-input.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 \

diff --git a/development/index.html b/development/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-call-gSV/blob/43f8249ad83a310fdade2b36178cf4abac0c73f9/README.md" class="icon icon-github"> Edit on GitHub</a>
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@@ -186,5 +186,5 @@ <h1 id="call-gsv">call-gSV</h1>
 
 <!--
 MkDocs version : 1.5.3
-Build Date UTC : 2024-05-02 21:16:26.346803+00:00
+Build Date UTC : 2024-05-07 18:13:41.493435+00:00
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diff --git a/development/inputs/index.html b/development/inputs/index.html
@@ -102,7 +102,7 @@
     <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-call-gSV/blob/43f8249ad83a310fdade2b36178cf4abac0c73f9/README.md" class="icon icon-github"> Edit on GitHub</a>
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@@ -257,7 +257,7 @@ <h3 id="nextflow-config-file-parameters">Nextflow Config File Parameters</h3>
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-<p>An example of the NextFlow Input Parameters Config file can be found <a href="https://github.com/uclahs-cds/pipeline-call-gSV/blob/1cf467fb660bb3cff75ed58c84187862fe61a690/config/template.config">here</a>.</p>
+<p>An example of the NextFlow Input Parameters Config file can be found <a href="https://github.com/uclahs-cds/pipeline-call-gSV/blob/43f8249ad83a310fdade2b36178cf4abac0c73f9/config/template.config">here</a>.</p>
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diff --git a/development/license/index.html b/development/license/index.html
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+          <a href="https://github.com/uclahs-cds/pipeline-call-gSV/blob/43f8249ad83a310fdade2b36178cf4abac0c73f9/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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+          <a href="https://github.com/uclahs-cds/pipeline-call-gSV/blob/43f8249ad83a310fdade2b36178cf4abac0c73f9/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
@@ -100,7 +100,7 @@
     <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-call-gSV/blob/43f8249ad83a310fdade2b36178cf4abac0c73f9/README.md" class="icon icon-github"> Edit on GitHub</a>
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@@ -153,7 +153,7 @@ <h3 id="node-specific-config-file-settings">Node Specific Config File Settings</
 </tbody>
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 <hr />
-<p>* Manta SV calling wouldn't work on an F2 node due to incompatible resources. In order to test the pipeline for tasks not relevant to Manta, please set <code>run_manta = false</code> in the sample specific <a href="https://github.com/uclahs-cds/pipeline-call-gSV/blob/1cf467fb660bb3cff75ed58c84187862fe61a690/config/template.config">config</a> file.</p>
+<p>* Manta SV calling wouldn't work on an F2 node due to incompatible resources. In order to test the pipeline for tasks not relevant to Manta, please set <code>run_manta = false</code> in the sample specific <a href="https://github.com/uclahs-cds/pipeline-call-gSV/blob/43f8249ad83a310fdade2b36178cf4abac0c73f9/config/template.config">config</a> file.</p>
 
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diff --git a/development/pipeline-steps/index.html b/development/pipeline-steps/index.html
@@ -112,7 +112,7 @@
     <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-gSV/blob/1cf467fb660bb3cff75ed58c84187862fe61a690/README.md" class="icon icon-github"> Edit on GitHub</a>
+          <a href="https://github.com/uclahs-cds/pipeline-call-gSV/blob/43f8249ad83a310fdade2b36178cf4abac0c73f9/README.md" class="icon icon-github"> Edit on GitHub</a>
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@@ -196,7 +196,7 @@ <h3 id="1-calling-structural-variants">1. Calling Structural Variants</h3>
 </table>
 <h3 id="2-calling-copy-number-variants">2. Calling Copy Number Variants</h3>
 <p>The second step of the pipeline identifies CNVs. To do this, Delly requires an aligned and sorted BAM file, as well as the BCF output from the SV calling step (to refine breakpoints) and a mappability map. Any CNVs identified are annotated and output as a single BCF file.</p>
-<p>Currently the following filters are applied by Delly when calling CNVs. Parameters with a "call-gSV default" can be updated in the sample specific nextflow <a href="https://github.com/uclahs-cds/pipeline-call-gSV/blob/1cf467fb660bb3cff75ed58c84187862fe61a690/config/template.config">config</a> file.
+<p>Currently the following filters are applied by Delly when calling CNVs. Parameters with a "call-gSV default" can be updated in the sample specific nextflow <a href="https://github.com/uclahs-cds/pipeline-call-gSV/blob/43f8249ad83a310fdade2b36178cf4abac0c73f9/config/template.config">config</a> file.
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+          <a href="https://github.com/uclahs-cds/pipeline-call-gSV/blob/43f8249ad83a310fdade2b36178cf4abac0c73f9/README.md" class="icon icon-github"> Edit on GitHub</a>
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+          <a href="https://github.com/uclahs-cds/pipeline-call-gSV/blob/43f8249ad83a310fdade2b36178cf4abac0c73f9/README.md" class="icon icon-github"> Edit on GitHub</a>
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diff --git a/versions.json b/versions.json
@@ -4,8 +4,8 @@
     "title": "development",
     "aliases": [],
     "properties": {
-      "commit": "1cf467fb660bb3cff75ed58c84187862fe61a690",
-      "date": "2024-05-02T14:15:36-07:00"
+      "commit": "43f8249ad83a310fdade2b36178cf4abac0c73f9",
+      "date": "2024-05-07T11:12:59-07:00"
     }
   },
   {