usage guides

• quickstart

  This is a quickstart guide that should get the pipeline running in most situations. A more detailed description of the structure of the parameters file and the command line usage is in the analysis configuration section.
• scamp configuration

  These notes illustrate how to configure an analysis using {scamp}. Detailed descriptions of the parameters can be found in the modules or workflows documentation.
• user-configurable parameters

  This post contains a more-detailed description of the parameters that are available to configure {scamp}. Some parameters are required, others may be defined from defaults while some may be provided by upstream {scamp} processes.