diff --git a/isoslam/processing.py b/isoslam/processing.py index 0e63be7..8226676 100644 --- a/isoslam/processing.py +++ b/isoslam/processing.py @@ -55,6 +55,8 @@ def create_parser() -> arg.ArgumentParser: subparsers = parser.add_subparsers(title="program", description="Available programs listed below:", dest="program") # Create sub-parsers for different stages + + # Process processes all files process_parser = subparsers.add_parser( "process", description="Process all files and run all summary plotting and statistics.", @@ -83,6 +85,33 @@ def create_parser() -> arg.ArgumentParser: "-v", "--vcf-file", dest="vcf_file", type=Path, required=False, help="Path to '.vcf.gz' file." ) process_parser.set_defaults(func=process) + + # Create configuration sub-parser + create_config_parser = subparsers.add_parser( + "create-config", + description="Create a configuration file using the defaults.", + help="Create a configuration file using the defaults.", + ) + create_config_parser.add_argument( + "-f", + "--filename", + dest="filename", + type=Path, + required=False, + default="config.yaml", + help="Name of YAML file to save configuration to (default 'config.yaml').", + ) + create_config_parser.add_argument( + "-o", + "--output-dir", + dest="output_dir", + type=Path, + required=False, + default="./", + help="Path to where the YAML file should be saved (default './' the current directory).", + ) + # create_config_parser.set_defaults(func=create_config) + # Additional parsers for future functionality # summarize_counts_parser = subparsers.add_parser( # "summarize",