def init_parser(parser):
    """Initialize parser args."""
    parser.add_argument(
        'marker', type=str,
        help=("Marker file input")
    )
    parser.add_argument(
        'vis', type=str,
        help=("vis file input")
    )
    parser.add_argument(
        'cluster', type=str,
        help=("Cluster file input")
    )
    parser.add_argument(
        '-g', nargs='?', default=None,
        help="Optional Gene list"
    )
    parser.add_argument(
        'output_path', type=str,
        help="the output directory where output files should go"
    )
    parser.add_argument(
        '-C', nargs='?', default=None,
        help="Num of cores avail for parallelization"
    )
    parser.add_argument(
        '-X', nargs='?', default=None,
        help="X argument for XL-mHG"
    )
    parser.add_argument(
        '-L', nargs='?', default=None,
        help="L argument for XL-mHG"
    )
    parser.add_argument(
        '-Abbrev', nargs='?',default=[],
        help="Choose between abbreviated or full 3-gene computation"
    )
    parser.add_argument(
        '-K', nargs='?',default=None,
        help="K-gene combinations to include"
    )
    parser.add_argument(
        '-Down', nargs='?',default=False,
        help="Downsample"
    )
    parser.add_argument(
        '-Trim', nargs='?',default=2000,
        help="Trim output files"
    )
    parser.add_argument(
        '-Count', nargs='?',default=False,
        help="Set to True when count data is being used, for visualizations."
    )
    parser.add_argument(
        '-tenx', nargs='?',default=False,
        help="Set to True when count data is being used, for visualizations."
    )
    parser.add_argument(
        '-online', nargs='?',default=False,
        help="Set to True for online version."
    )
    parser.add_argument(
        '-skipvis', nargs='?',default=False,
        help="Set to True to skip visualizations."
    )
    return parser