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| <h1 id="welcome-to-asarusim">Welcome to AsaruSim</h1> | ||
| <p>AsaruSim is an automated <a href="https://www.nextflow.io/">Nextflow</a> workflow designed for simulating 10x single-cell Nanopore reads. It allows to benchmark and optimize single-cell Nanopore long read data processing pipelines.</p> | ||
| <p>Github repository <a href="https://github.com/alihamraoui/AsaruSim">AsaruSim</a>.</p> | ||
| <h2 id="requirements">Requirements</h2> | ||
| <ul> | ||
| <li><code>Nextflow</code> - A workflow engine for complex data pipelines.</li> | ||
| <li><code>Docker</code> or <code>Singularity</code> - Containers for packaging necessary software, ensuring reproducibility.</li> | ||
| </ul> | ||
| <h2 id="install-nextflow">Install nextflow</h2> | ||
| <p>Ensure you have the following installed on your system:</p> | ||
| <p><code>Java 8 or later</code>: Nextflow requires Java. Install it from Oracle or use a package manager like apt, brew, or yum depending on your OS.</p> | ||
| <pre><code class="language-bash">curl -s https://get.nextflow.io | bash | ||
| chmod +x nextflow | ||
| sudo mv nextflow /usr/local/bin/ | ||
| </code></pre> | ||
| <p>Nextflow is now installed and ready to use on your system. For further details on using Nextflow, refer to the <a href="https://www.nextflow.io/docs/latest/index.html">official documentation</a>.</p> | ||
| <h2 id="install-docker">Install docker</h2> | ||
| <p><a href="https://docs.docker.com/engine/install/">Install Docker</a>.</p> | ||
| <h2 id="run-asarusim">Run AsaruSim</h2> | ||
| <ul> | ||
| <li>1 - Clone the github repository</li> | ||
| </ul> | ||
| <pre><code class="language-bash">git clone https://github.com/alihamraoui/AsaruSim.git | ||
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| cd AsaruSim | ||
| </code></pre> | ||
| <ul> | ||
| <li>2 - Run using nextflow</li> | ||
| </ul> | ||
| <pre><code class="language-bash">nextflow run main.nf --help | ||
| </code></pre> | ||
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