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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -106,7 +106,7 @@ | |
| <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-sSV/blob/9690887a9b1e89c56f93937a4806f0cca5e08ce1/README.md" class="icon icon-github"> Edit on GitHub</a> | ||
| <a href="https://github.com/uclahs-cds/pipeline-call-sSV/blob/5cbd522d8ce4c514ecbba20d645b101808b4e083/README.md" class="icon icon-github"> Edit on GitHub</a> | ||
| </li> | ||
| </ul> | ||
| <hr/> | ||
|
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@@ -128,13 +128,13 @@ <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-sSV/blob/9690887a9b1e89c56f93937a4806f0cca5e08ce1/config/template.config">here</a>. See <a href="../nextflow-config-file-parameters/#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-sSV/blob/5cbd522d8ce4c514ecbba20d645b101808b4e083/config/template.config">here</a>. See <a href="../nextflow-config-file-parameters/#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-sSV/blob/9690887a9b1e89c56f93937a4806f0cca5e08ce1/input/call-sSV-input.yaml">template</a>.See <a href="../inputs/#Input-YAML">Input YAML</a> for detailed description of each column.</p> | ||
| <p>Create the input YAML using the <a href="https://github.com/uclahs-cds/pipeline-call-sSV/blob/5cbd522d8ce4c514ecbba20d645b101808b4e083/input/call-sSV-input.yaml">template</a>.See <a href="../inputs/#Input-YAML">Input YAML</a> for detailed description of each column.</p> | ||
| </li> | ||
| <li> | ||
| <p>Again, do not directly modify the source template input YAML file. Instead, copy it from the pipeline release folder to your project-specific folder and modify it there.</p> | ||
|
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@@ -150,8 +150,8 @@ <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-sSV/Nextflow/release/6.0.0-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-sSV/blob/9690887a9b1e89c56f93937a4806f0cca5e08ce1/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-sSV/blob/9690887a9b1e89c56f93937a4806f0cca5e08ce1/input/call-sSV-input.yaml">input-sSV.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-sSV/blob/5cbd522d8ce4c514ecbba20d645b101808b4e083/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-sSV/blob/5cbd522d8ce4c514ecbba20d645b101808b4e083/input/call-sSV-input.yaml">input-sSV.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 \ | ||
|
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@@ -163,7 +163,7 @@ <h3 id="run-steps">Run steps</h3> | |
| --email <your UCLA email, [email protected]> | ||
| </code></pre> | ||
| <p>In the above command, the partition type can be changed based on the size of the dataset. At this point, node F16 is generally recommended for larger datasets like A-full and node F2 for smaller datasets like A-mini.</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>algorithm = ['delly']</code> in the sample specific <a href="https://github.com/uclahs-cds/pipeline-call-sSV/blob/9690887a9b1e89c56f93937a4806f0cca5e08ce1/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>algorithm = ['delly']</code> in the sample specific <a href="https://github.com/uclahs-cds/pipeline-call-sSV/blob/5cbd522d8ce4c514ecbba20d645b101808b4e083/config/template.config">config</a> file.</p> | ||
| <blockquote> | ||
| <p><strong>Note</strong>: Because this pipeline uses an image stored in the GitHub Container Registry, you must follow the steps listed in the <a href="https://uclahs-cds.atlassian.net/wiki/spaces/BOUTROSLAB/pages/3190419/Docker+Introduction#DockerIntroduction-HowtosetupPATandlogintotheregistryHowtosetupPATandlogintotheregistry">Docker Introduction</a> on Confluence to set up a PAT for your GitHub account and log into the registry on the cluster before running this pipeline.</p> | ||
| </blockquote> | ||
|
|
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