INNER CODE UNIT · Python

_get_args

nf-core/eager · bin/kraken_parse.py:9

def _get_args():
    '''This function parses and return arguments passed in'''
    parser = argparse.ArgumentParser(
        prog='kraken_parse',
        formatter_class=argparse.RawDescriptionHelpFormatter,
        description='Parsing kraken')
    parser.add_argument('krakenReport', help="path to kraken report file")
    parser.add_argument(
        '-c',
        dest="count",
        default=50,
        help="Minimum number of hits on clade to report it. Default = 50")
    parser.add_argument(
        '-or',
        dest="readout",
        default=None,
        help="Read count output file. Default = <basename>.read_kraken_parsed.csv")
    parser.add_argument(

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