INNER CODE UNIT · Python

_get_args

nf-core/eager · bin/extract_map_reads.py:14

def _get_args():
    """This function parses and return arguments passed in"""
    parser = argparse.ArgumentParser(
        prog="extract_mapped_reads",
        formatter_class=argparse.RawDescriptionHelpFormatter,
        description="Remove mapped in bam file from fastq files",
    )
    parser.add_argument("bam_file", help="path to bam file")
    parser.add_argument("fwd", help="path to forward fastq file")
    parser.add_argument(
        "-merged",
        dest="merged",
        default=False,
        action="store_true",
        help="specify if bam file was created from merged fastq files",
    )
    parser.add_argument(
        "-rev", dest="rev", default=None, help="path to reverse fastq file"

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