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<!DOCTYPE html>
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<title>Using GGD in Workflows — GGD documentation</title>
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<li class="toctree-l1 current"><a class="current reference internal" href="#">Using GGD in Workflows</a><ul>
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<li class="toctree-l2"><a class="reference internal" href="#snakemake-workflow-example"><span class="xref std std-ref">Snakemake Workflow Example</span></a></li>
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<div class="section" id="using-ggd-in-workflows">
<span id="workflows"></span><h1>Using GGD in Workflows<a class="headerlink" href="#using-ggd-in-workflows" title="Permalink to this headline">¶</a></h1>
<p>[<a class="reference internal" href="index.html#home-page"><span class="std std-ref">Click here to return to the home page</span></a>]</p>
<div class="admonition important">
<p class="admonition-title">Important</p>
<p>If you use GGD, please cite the <a class="reference external" href="https://www.nature.com/articles/s41467-021-22381-z">Nature Communications GGD paper</a></p>
</div>
<div class="section" id="ggd-and-workflows">
<h2>GGD and Workflows<a class="headerlink" href="#ggd-and-workflows" title="Permalink to this headline">¶</a></h2>
<p>Another advantage of GGD is its ability to be used in different workflows. These workflows can range from simple to complex, as well as from a bash
script style workflow to more advance worflow managers like Snakemake and Nextflow.</p>
<p>It is customary that data is required and used during a workflow. Rather then having to store and transmit that data along with a workflow, one
could create the workflow with GGD data packages as dependencies and allow GGD to dynamically provide the data to the workflow.</p>
<p>GGD can be used before running a workflow or during the workflow process. Additionaly, data recipes can be installed into a Docker or Singularity
container, where a workflow like Netxflow uses the conda software packages and the GGD data packages in the container during the workflow process.
GGD can be used during the workflow to install the required package into a specific environment if those packages are not yet installed. This allows
versitlity in the use of GGD for many types of workflows.</p>
<p>Provided below are two examples of using GGD in a workflow. These are two simple exmaples and don’t fully show the extent of what can be done with GGD
wihtin a workflow, but rather stand as starting examples of what can be done.</p>
</div>
<div class="section" id="snakemake-workflow-example">
<h2><a class="reference internal" href="snakemake_workflow.html#snakemake-workflow"><span class="std std-ref">Snakemake Workflow Example</span></a><a class="headerlink" href="#snakemake-workflow-example" title="Permalink to this headline">¶</a></h2>
</div>
<div class="section" id="nextflow-workflow-example">
<h2><a class="reference internal" href="nextflow_workflow.html#nextflow-workflow"><span class="std std-ref">Nextflow Workflow Example</span></a><a class="headerlink" href="#nextflow-workflow-example" title="Permalink to this headline">¶</a></h2>
<p>Contents:</p>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="snakemake_workflow.html">Snakemake Workflow with GGD</a><ul>
<li class="toctree-l2"><a class="reference internal" href="snakemake_workflow.html#workflow-files">Workflow Files</a></li>
<li class="toctree-l2"><a class="reference internal" href="snakemake_workflow.html#alternative-approaches">Alternative Approaches</a></li>
<li class="toctree-l2"><a class="reference internal" href="snakemake_workflow.html#workflow-output-examples">Workflow Output Examples:</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="nextflow_workflow.html">Nextflow Workflow with GGD</a><ul>
<li class="toctree-l2"><a class="reference internal" href="nextflow_workflow.html#nextflow-workflow-files">Nextflow Workflow Files</a></li>
<li class="toctree-l2"><a class="reference internal" href="nextflow_workflow.html#steps-to-run-the-workflow">Steps to run the workflow</a></li>
<li class="toctree-l2"><a class="reference internal" href="nextflow_workflow.html#results">Results:</a></li>
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