# parser.add_argument("-f", "--file", help="create overlay for a single file",
parser.add_argument('-i','--input',nargs='?',default='.',help='Input MDOC file to process.')
parser.add_argument('-d','--outDir',nargs='?',default='.',help='Optional output directory to write scripts to.')
parser.add_argument('-dp','--dataPath',nargs='?',default='.',help='Optional override to use if the data is mounted in a different network base path.')
parser.add_argument('-cp','--clusterPath',nargs='?',default='/projects/project-nieverge/',help='Destination path of the HPC filesystem data directory.')
# parser.add_argument('-dp', '--dataPath', nargs='?', default='.', help='Optional override to use if the data is mounted in a different network base path.')
# parser.add_argument('-cp', '--clusterPath', nargs='?', default='/projects/project-nieverge/', help='Destination path of the HPC filesystem data directory.')
parser.add_argument('-cv','--cudaVer',nargs='?',type=int,default=92,help='Override CUDA version. Default 92. Reduce to a lower value if MotionCor2 does not run properly with the installed graphics card.')
parser.add_argument('-ps','--patchSize',nargs='?',type=int,default=3,help='Override local alignment patch count. Default 3.')
parser.add_argument('-b','--binning',nargs='?',type=int,default=1,help='Output binning. Default 1 (no binning).')