def main(): a = argparser() a.add_argument('--run_name', type=str) args = a.parse_args() log_cfg.add_handler(FileHandler(args.log_file)) action = CreateReagentForRun(args.step_uri, args.username, args.password, args.run_name) return action.run()
def _parse_args(): p = argparser() p.add_argument('--format', dest='format', type=str, choices=['igmm', 'quantStudio'], help='The format of the genotype file') p.add_argument('--input_genotypes', dest='input_genotypes', type=str, help='The file that contains the genotype for all the samples (For testing only)') p.add_argument('--genotypes_artifact_id', dest='genotypes_artifact_id', type=str, help='The id of the output artifact that contains the output file') p.add_argument('--no_upload', dest='no_upload', action='store_true', help='Prevent any upload to the LIMS') return p.parse_args()
def main(): p = argparser() p.add_argument('--workflow', dest='workflow', type=str, required=True, help='The name of the workflow we should route the artifacts to.') p.add_argument('--stage', dest='stage', type=str, help='The name of the stage in the workflow we should route the artifacts to.') p.add_argument('--source', dest='source', type=str, required=True, choices=['input', 'output', 'submitted'], help='The name of the stage in the workflow we should route the artifacts to.') args = p.parse_args() action = AssignWorkflowStage( args.step_uri, args.username, args.password, args.log_file, args.workflow, args.stage, args.source ) action.run()
def main(): args = argparser().parse_args() log_cfg.add_handler(FileHandler(args.log_file)) action = FindPlateToRoute(args.step_uri, args.username, args.password, args.log_file) return action.run()