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=== Defining a New Pipeline ===
=== Defining a New Pipeline ===
<ol>
<li> Define a new configuration section for your pipeline
<ul><li> Example:</li></ul>
<dd> <pre>[pipelineName]</pre>
</li>
<li>Define the steps in this pipeline using the key <code>STEPS</code> under that section
<ul><li> Example:</li></ul>
<dd><pre>[pipelineName]
STEPS = stepName1 stepName2 stepName3</pre>
<ul><li> Note: each step must have its own configuration section</li></ul>
</li>
<li>Create a section for each step
<ul><li> Example:
<dd> <pre>[stepName1]</pre>
</li>
</ul>
<ol>
<li>Set required keys for each step:
<ol>
<li><code>DEPEND</code> - dependencies for this step
<dd> Valid Values (separate multiple dependencies with a space):
<ul>
<li><code>BAM</code></li>
<li>Name of step that must complete prior to this step</li>
<li></li>
</ul>
</li>
<li><code>OUTPUT</code> - name of output file
</li>
<li><code>CMD</code> - command for running the step
</li>
</ol>
</li>
</ol>
</li>
</ol>
