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1. The top-level root element in the configuration file is a pipeline. Define the name and type attributes, and the dataset-base-path and run-log-path elements. The type attribute must be from a finite set of values which are listed below. The dataset-base-path is simply a convenient prefix for the files you define in step 4.
2. Define the list of executables your pipeline will run. This section simply gives a friendly name and a version string (which is used for documentation purposes only) to the long absolute file paths that executables typically have. You refer to these executables by their friendly names in the processing-step elements defined below in step 6.
3. Define the batch job configurations your pipeline needs. This section simply gives a friendly name to a batch queue, batch group, 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 6. The queue and group attributes must be from a finite set of values which are listed below.
4. Define the list of files your pipeline is concerned with using file elements. This section simply gives friendly names to long file paths and defines some meta-information about the files. You refer to these files by their friendly names in the processing-step elements defined below in step 6. The type and file-type attributes must be from a finite set of values which are listed below. The file paths are directories that are relative to dataset-base-path defined in step 1.
5. Define the list of input files from other pipelines that you want to use as input to your pipeline using foreign-input-file elements. This section simply gives friendly names to files produced by other pipelines (hence the name "foreign"). You refer to these files by their friendly names in the processing-step elements defined below in step 6. The pipeline attribute specifies the name of the pipeline that produced the file you want to use as input. The file attribute specifies the name given to the file in the "foreign" pipeline (this is the names used in step 4).
6. Finally, define the processing steps of your pipeline. 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 steps 4 and 5) in the list of input-file and output-file elements. You can refer to both the file elements defined in step 4, or the foreign-input-file elements defined in step 45.

Example Configuration File

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