Allow the pipeline configuration to define command line arguments that are not displayed in the help message. This would allow the parameter sets to access the argument and thus define arguments that the user can't touch. This is useful for many pipelines, for example, performing an intersection to generate the unique portion of a file requires setting the flag '--invert'. This should always be set, so can be given an argument in the configuration file and the default value can be set to 'set', so that it is always used. When viewing the help, the message isn't cluttered with this information.
Allow the pipeline configuration to define command line arguments that are not displayed in the help message. This would allow the parameter sets to access the argument and thus define arguments that the user can't touch. This is useful for many pipelines, for example, performing an intersection to generate the unique portion of a file requires setting the flag '--invert'. This should always be set, so can be given an argument in the configuration file and the default value can be set to 'set', so that it is always used. When viewing the help, the message isn't cluttered with this information.