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| Original file line number | Diff line number | Diff line change |
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| <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-align-DNA/blob/ddd326a3cbc7b9a4451dc0211c0938826929552d/README.md" class="icon icon-github"> Edit on GitHub</a> | ||
| <a href="https://github.com/uclahs-cds/pipeline-align-DNA/blob/a7cfae754d4315a5f6204c1ad13b0535717fc3b4/README.md" class="icon icon-github"> Edit on GitHub</a> | ||
| </li> | ||
| </ul> | ||
| <hr/> | ||
|
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@@ -126,13 +126,13 @@ <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>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-align-DNA/blob/ddd326a3cbc7b9a4451dc0211c0938826929552d/config/template.config">here</a>. See <a href="../inputs/#Inputs">Inputs</a> for the detailed description of each variable in the config file. The config file can be generated using a python script (see below).</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-align-DNA/blob/a7cfae754d4315a5f6204c1ad13b0535717fc3b4/config/template.config">here</a>. See <a href="../inputs/#Inputs">Inputs</a> for the detailed description of each variable in the config file. The config file can be generated using a python script (see below).</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 csv using the <a href="https://github.com/uclahs-cds/pipeline-align-DNA/blob/ddd326a3cbc7b9a4451dc0211c0938826929552d/input/align-DNA.input.csv">template</a>. The example csv is a single-lane sample, however this pipeline can take multi-lane sample as well, with each record in the csv file representing a lane (a pair of fastq). All records must have the same value in the <strong>sample</strong> column. See <a href="../inputs/#Inputs">Inputs</a> for detailed description of each column. All columns must exist in order to run the pipeline successfully.</p> | ||
| <p>Create the input csv using the <a href="https://github.com/uclahs-cds/pipeline-align-DNA/blob/a7cfae754d4315a5f6204c1ad13b0535717fc3b4/input/align-DNA.input.csv">template</a>. The example csv is a single-lane sample, however this pipeline can take multi-lane sample as well, with each record in the csv file representing a lane (a pair of fastq). All records must have the same value in the <strong>sample</strong> column. See <a href="../inputs/#Inputs">Inputs</a> for detailed description of each column. All columns must exist in order to run the pipeline successfully.</p> | ||
| </li> | ||
| <li> | ||
| <p>Again, do not directly modify the source template csv file. Instead, copy it from the pipeline release folder to your project-specific folder and modify it there.</p> | ||
|
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@@ -145,7 +145,7 @@ <h2 id="how-to-run">How To Run</h2> | |
| </code></pre> | ||
| <ul> | ||
| <li>For example, <code>path/to/main.nf</code> could be: <code>/hot/software/pipeline/pipeline-align-DNA/Nextflow/release/8.0.0/pipeline/align-DNA.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-align-DNA/blob/ddd326a3cbc7b9a4451dc0211c0938826929552d/config/template.config">template.config</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-align-DNA/blob/a7cfae754d4315a5f6204c1ad13b0535717fc3b4/config/template.config">template.config</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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@@ -156,7 +156,7 @@ <h2 id="how-to-run">How To Run</h2> | |
| --email [email protected] | ||
| </code></pre> | ||
| <p><b><i> BWA-MEM2 Genome Index </i></b> | ||
| The reference genome index must be generated by BWA-MEM2 with the correct version. Genome index generated by old BWA-MEM2 versions or the original BWA is not accepted. The reference genome index can be generated using the <a href="https://github.com/uclahs-cds/pipeline-align-DNA/blob/ddd326a3cbc7b9a4451dc0211c0938826929552d/module/generate-genome-index.nf"><code>generate-genome-index.nf</code></a> nextflow pipeline. To run this pipeline, you need to create a config file using this <a href="https://github.com/uclahs-cds/pipeline-align-DNA/blob/ddd326a3cbc7b9a4451dc0211c0938826929552d/config/index.config">template</a> to specify the path of <code>reference_fasta</code> and the <code>temp_dir</code>. The <code>temp_dir</code> is used to store intermediate files of Nextflow. The genome index files are saved to the same directory of the input reference FASTA by the pipeline. Use the command below to run this generate genome index pipeline:</p> | ||
| The reference genome index must be generated by BWA-MEM2 with the correct version. Genome index generated by old BWA-MEM2 versions or the original BWA is not accepted. The reference genome index can be generated using the <a href="https://github.com/uclahs-cds/pipeline-align-DNA/blob/a7cfae754d4315a5f6204c1ad13b0535717fc3b4/module/generate-genome-index.nf"><code>generate-genome-index.nf</code></a> nextflow pipeline. To run this pipeline, you need to create a config file using this <a href="https://github.com/uclahs-cds/pipeline-align-DNA/blob/a7cfae754d4315a5f6204c1ad13b0535717fc3b4/config/index.config">template</a> to specify the path of <code>reference_fasta</code> and the <code>temp_dir</code>. The <code>temp_dir</code> is used to store intermediate files of Nextflow. The genome index files are saved to the same directory of the input reference FASTA by the pipeline. Use the command below to run this generate genome index pipeline:</p> | ||
| <pre><code class="language-bash">nextflow run path/to/generate-genome-index.nf -config path/to/genome-specific.config | ||
| </code></pre> | ||
| <p>This can also be submitted using the <a href="https://github.com/uclahs-cds/tool-submit-nf">submission script</a> to the UCLAHS-CDS's Azure cloud as mentioned above.</p> | ||
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