This is the main function for ProTECT.

def main():
    """
    This is the main function for ProTECT.
    """
    parser = argparse.ArgumentParser(prog='ProTECT',
                                     description='Prediction of T-Cell Epitopes for Cancer Therapy',
                                     epilog='Contact Arjun Rao (aarao@ucsc.edu) if you encounter '
                                     'any problems while running ProTECT')
    inputs = parser.add_mutually_exclusive_group(required=True)
    inputs.add_argument('--config_file', dest='config_file', help='Config file to be used in the '
                        'run.', type=str, default=None)
    inputs.add_argument('--generate_config', dest='generate_config', help='Generate a config file '
                        'in the current directory that is pre-filled with references and flags for '
                        'an hg19 run.', action='store_true', default=False)
    parser.add_argument('--max-cores-per-job', dest='max_cores', help='Maximum cores to use per '
                        'job. Aligners and Haplotypers ask for cores dependent on the machine that '
                        'the launchpad gets assigned to -- In a heterogeneous cluster, this can '
                        'lead to problems. This value should be set to the number of cpus on the '
                        'smallest node in a cluster.',
                        type=int, required=False, default=None)
    # We parse the args once to see if the user has asked for a config file to be generated.  In
    # this case, we don't need a jobstore.  To handle the case where Toil arguments are passed to
    # ProTECT, we parse known args, and if the used specified config_file instead of generate_config
    # we re-parse the arguments with the added Toil parser.
    params, others = parser.parse_known_args()
    if params.generate_config:
        generate_config_file()
    else:
        Job.Runner.addToilOptions(parser)
        params = parser.parse_args()
        params.config_file = os.path.abspath(params.config_file)
        if params.maxCores:
            if not params.max_cores:
                params.max_cores = int(params.maxCores)
            else:
                if params.max_cores > int(params.maxCores):
                    print("The value provided to max-cores-per-job (%s) was greater than that "
                          "provided to maxCores (%s). Setting max-cores-per-job = maxCores." %
                          (params.max_cores, params.maxCores), file=sys.stderr)
                    params.max_cores = int(params.maxCores)
        start = Job.wrapJobFn(parse_config_file, params.config_file, params.max_cores)
        Job.Runner.startToil(start, params)
    return None