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Here are the steps you should take to create an xml configuration file to define a pipeline:

1. The top-level root element in the configuration file is a pipeline. Define the type attribute, and the base-path and run-log-path for your pipeline elements. The type attribute must be from a finite set that we define which are listed below.
2. Define the list of executables your pipeline will run in the executable-list section. This section simply gives a friendly name and a version string (which is used for documentation purposes only) to the long file paths of the executables your pipeline will run. You refer to these executables by their friendly names in the processing-step elements defined below in step 5.
3. Define the batch job configurations your pipeline needs in the batch-job-configuration-list section. This section simply gives a friendly name to a batch queue, a working directory and the directory where the log file will go. You refer to these batch job configurations by their friendly names in the processing-step elements defined below in step 5. The queue attribute must be from a finite set that we define which are listed below. The working-directory and log-file-path elements are directories that are relative to base-path defined in step 1.
4. Define the list of files your pipeline is concerned with in the file-list section. This section simply gives friendly names to long files paths and defines some meta-information about the files. You refer to these files by their friendly names in the input-file-list and output-file-list sections in the processing-step elements defined below in step 5. The type and file-type attributes must be from a finite set that we define which are listed below.
5. Finally, define the processing steps of your pipeline in the processing-step-list section. Each processing-step in this section refers to the executable defined in step 2 (via the executable attribute), the batch job configuration defined in step 3 (via the batch-job-configuration attribute), and the list of input files and output files (which you defined in step 4) in the input-file-list and output-file-list sections, respectively.

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