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uclahs-cds · Jun 28, 2024 · 24e54f5 · 24e54f5
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diff --git a/development/contributors/index.html b/development/contributors/index.html
@@ -98,7 +98,7 @@
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       <li class="breadcrumb-item active">Contributors</li>
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-          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/11d66229e54efcefe6b9620126e00829835d3065/README.md" class="icon icon-github"> Edit on GitHub</a>
+          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/e801e93e55fdf772bd39214af4cd979c328734fb/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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+          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/e801e93e55fdf772bd39214af4cd979c328734fb/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 @@
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+          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/e801e93e55fdf772bd39214af4cd979c328734fb/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/11d66229e54efcefe6b9620126e00829835d3065/README.md" class="icon icon-github"> Edit on GitHub</a>
+          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/e801e93e55fdf772bd39214af4cd979c328734fb/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/11d66229e54efcefe6b9620126e00829835d3065/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/e801e93e55fdf772bd39214af4cd979c328734fb/config/template.config">Example config</a>).</p>
 </li>
 <li>
-<p>Update the YAML (<a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/11d66229e54efcefe6b9620126e00829835d3065/input">Template YAMLs</a>).</p>
+<p>Update the YAML (<a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/e801e93e55fdf772bd39214af4cd979c328734fb/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/e801e93e55fdf772bd39214af4cd979c328734fb/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>
 
 <!--
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-Build Date UTC : 2024-06-25 20:42:31.948305+00:00
+Build Date UTC : 2024-06-28 17:21:15.918730+00:00
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diff --git a/development/inputs/index.html b/development/inputs/index.html
@@ -106,7 +106,7 @@
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+          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/e801e93e55fdf772bd39214af4cd979c328734fb/README.md" class="icon icon-github"> Edit on GitHub</a>
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@@ -295,39 +295,107 @@ <h3 id="config">Config</h3>
 <td style="text-align: left;">Path of working directory for Nextflow. When included in the sample config file, Nextflow intermediate files and logs will be saved to this directory. With ucla_cds, the default is <code>/scratch</code> and should only be changed for testing/development. Changing this directory to <code>/hot</code> or <code>/tmp</code> can lead to high server latency and potential disk space limitations, respectively.</td>
 </tr>
 <tr>
-<td style="text-align: left;"><code>docker_container_registry</code></td>
+<td style="text-align: left;"><code>base_resource_update</code></td>
 <td style="text-align: left;">optional</td>
-<td style="text-align: left;">string</td>
-<td style="text-align: left;">Registry containing tool Docker images. Default: <code>ghcr.io/uclahs-cds</code></td>
+<td style="text-align: left;">namespace</td>
+<td style="text-align: left;">Namespace of parameters to update base resource allocations in the pipeline. Usage and structure are detailed in <code>template.config</code> and below.</td>
+</tr>
+</tbody>
+</table>
+<p>The below parameters have default values defined in <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/e801e93e55fdf772bd39214af4cd979c328734fb/config/default.config"><code>default.config</code></a> and generally do not need to be set by the user.</p>
+<table>
+<thead>
+<tr>
+<th style="text-align: left;">Optional Parameter</th>
+<th style="text-align: left;">Type</th>
+<th style="text-align: left;">Description</th>
 </tr>
+</thead>
+<tbody>
 <tr>
 <td style="text-align: left;"><code>metapipeline_delete_input_bams</code></td>
-<td style="text-align: left;">optional</td>
 <td style="text-align: left;">boolean</td>
 <td style="text-align: left;">Set to true to delete the input BAM files once the initial processing step is complete. <strong>WARNING</strong>: This option should NOT be used for individual runs of recalibate-BAM; it's intended for metapipeline-DNA to optimize disk space usage by removing files that are no longer needed from the <code>workDir</code>.</td>
 </tr>
 <tr>
 <td style="text-align: left;"><code>metapipeline_final_output_dir</code></td>
-<td style="text-align: left;">optional</td>
 <td style="text-align: left;">string</td>
 <td style="text-align: left;">Absolute path for the final output directory of metapipeline-DNA that's expected to contain the output BAM from align-DNA. <strong>WARNING</strong>: This option should not be used for individual runs of recalibrate-BAM; it's intended for metapipeline-DNA to optimize disk space usage.</td>
 </tr>
 <tr>
 <td style="text-align: left;"><code>metapipeline_states_to_delete</code></td>
-<td style="text-align: left;">optional</td>
 <td style="text-align: left;">list</td>
 <td style="text-align: left;">List of states for which to delete input BAMs. <strong>WARNING</strong>: This option should not be used for individual runs of recalibrate-BAM; it's intended for metapipeline-DNA to optimize disk space usage.</td>
 </tr>
 <tr>
-<td style="text-align: left;"><code>base_resource_update</code></td>
-<td style="text-align: left;">optional</td>
-<td style="text-align: left;">namespace</td>
-<td style="text-align: left;">Namespace of parameters to update base resource allocations in the pipeline. Usage and structure are detailed in <code>template.config</code> and below.</td>
+<td style="text-align: left;"><code>cache_intermediate_pipeline_steps</code></td>
+<td style="text-align: left;">boolean</td>
+<td style="text-align: left;">Enable process caching from Nextflow.</td>
+</tr>
+<tr>
+<td style="text-align: left;"><code>ucla_cds</code></td>
+<td style="text-align: left;">boolean</td>
+<td style="text-align: left;">Overwrite default memory and CPU values by cluster-specific configs.</td>
+</tr>
+<tr>
+<td style="text-align: left;"><code>docker_container_registry</code></td>
+<td style="text-align: left;">string</td>
+<td style="text-align: left;">Registry containing tool Docker images.</td>
+</tr>
+<tr>
+<td style="text-align: left;"><code>docker_image_gatk</code>, <code>gatk_version</code></td>
+<td style="text-align: left;">string</td>
+<td style="text-align: left;">Docker image name and version for GATK.</td>
+</tr>
+<tr>
+<td style="text-align: left;"><code>docker_image_pipeval</code>, <code>pipeval_version</code></td>
+<td style="text-align: left;">string</td>
+<td style="text-align: left;">Docker image name and version for PipeVal.</td>
+</tr>
+<tr>
+<td style="text-align: left;"><code>docker_image_gatk3</code>, <code>gatk3_version</code></td>
+<td style="text-align: left;">string</td>
+<td style="text-align: left;">Docker image name and version for GATK3.</td>
+</tr>
+<tr>
+<td style="text-align: left;"><code>docker_image_picard</code>, <code>picard_version</code></td>
+<td style="text-align: left;">string</td>
+<td style="text-align: left;">Docker image name and version for Picard.</td>
+</tr>
+<tr>
+<td style="text-align: left;"><code>docker_image_samtools</code>, <code>samtools_version</code></td>
+<td style="text-align: left;">string</td>
+<td style="text-align: left;">Docker image name and version for SAMtools.</td>
+</tr>
+<tr>
+<td style="text-align: left;"><code>reference_fasta_fai</code>, <code>reference_fasta_dict</code></td>
+<td style="text-align: left;">path</td>
+<td style="text-align: left;">Index and dictionary files for the required input. Default: Matching <code>.fai</code> and <code>.dict</code> files in the same directory.</td>
+</tr>
+<tr>
+<td style="text-align: left;"><code>bundle_v0_dbsnp138_vcf_gz_tbi</code></td>
+<td style="text-align: left;">path</td>
+<td style="text-align: left;">Index file for the required input. Default: Matching <code>.tbi</code> file in the same directory.</td>
+</tr>
+<tr>
+<td style="text-align: left;"><code>bundle_known_indels_vcf_gz_tbi</code></td>
+<td style="text-align: left;">path</td>
+<td style="text-align: left;">Index file for the required input. Default: Matching <code>.tbi</code> file in the same directory.</td>
+</tr>
+<tr>
+<td style="text-align: left;"><code>bundle_contest_hapmap_3p3_vcf_gz_tbi</code></td>
+<td style="text-align: left;">path</td>
+<td style="text-align: left;">Index file for the required input. Default: Matching <code>.tbi</code> file in the same directory.</td>
+</tr>
+<tr>
+<td style="text-align: left;"><code>bundle_mills_and_1000g_gold_standard_indels_vcf_gz_tbi</code></td>
+<td style="text-align: left;">path</td>
+<td style="text-align: left;">Index file for the required input. Default: Matching <code>.tbi</code> file in the same directory.</td>
 </tr>
 </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/11d66229e54efcefe6b9620126e00829835d3065/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/e801e93e55fdf772bd39214af4cd979c328734fb/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/e801e93e55fdf772bd39214af4cd979c328734fb/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 @@
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+          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/e801e93e55fdf772bd39214af4cd979c328734fb/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 @@
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+          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/e801e93e55fdf772bd39214af4cd979c328734fb/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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+          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/e801e93e55fdf772bd39214af4cd979c328734fb/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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+          <a href="https://github.com/uclahs-cds/pipeline-recalibrate-BAM/blob/e801e93e55fdf772bd39214af4cd979c328734fb/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
@@ -4,8 +4,8 @@
     "title": "development",
     "aliases": [],
     "properties": {
-      "commit": "11d66229e54efcefe6b9620126e00829835d3065",
-      "date": "2024-06-25T13:41:56-07:00"
+      "commit": "e801e93e55fdf772bd39214af4cd979c328734fb",
+      "date": "2024-06-28T10:20:37-07:00"
     }
   },
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