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, 13:52, 9 March 2015
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| </ul> | | </ul> |
| === Defining a New Pipeline === | | === Defining a New Pipeline === |
− | # Define a new configuration section for your pipeline
| + | <ol> |
− | #: <code>[pipelineName]</code>
| + | <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> |