command_line_flags.txt

-f	required	input_file	a fully qualified path/name for the input file
-g	required	disease_group	the id or name of the disease group of the cohort being processed
-t	required	document_type	the type of clinical documents being processed (e.g. pathology reports)
-o	required	output_file	a fully qualified path/name for the output file
-a	not_required	no_algorithm_flag	this flag takes an optional boolean ('y'=run appropriate algorithms, 'n'=do not run any algorithms) default value is y
-ml	not_required	machine_learning_flag	this flag takes an optional boolean ('y'=run appropriate ml algorithms, 'n'=do not run any ml algorithms) default value is n
-sg	not_required	sub_disease_group	the id or name of the subdisease group (used for some algorithms)