@@ -35,23 +35,17 @@ def main(raw_args=None):
3535 parser .add_argument ("--innerprimer" , metavar = "enrichment_primers.txt" ,
3636 nargs = '?' , action = "store" , type = str ,
3737 help = "Text file containing one primer per line if non-10x inner enrichment primers were used" )
38- #parser.add_argument("-f", "--force", action="store_true",
39- # help="Use force-cells flag instead of expect-cells")
4038 group_cell_number = parser .add_mutually_exclusive_group ()
4139 group_cell_number .add_argument ("--force" , action = "store_true" ,
4240 help = "Use force-cells flag instead of expect-cells " )
4341 group_cell_number .add_argument ("--expect" , action = "store_true" ,
4442 help = "Run Cell Ranger with --expect-cells" )
45- #parser.add_argument("-i", "--introns", action="store_true",
46- # help="Use include-introns flag")
47- ## Since cellranger v7.0.0+, include-introns is true by default
4843 parser .add_argument ("-i" , "--exclude_introns" , action = "store_true" ,
4944 help = "Use include-introns,false option" )
5045 parser .add_argument ("--create_bam" , action = "store_true" ,
5146 help = "Use create_bam,true option" )
5247 parser .add_argument ("--disable_lib_check" , action = "store_true" ,
5348 help = "Use check-library-compatibility,false option (default option)" )
54- ## Fix RNA profiling parameters
5549 parser .add_argument ("--probe_set" , type = str ,
5650 help = "Text files containing probe sets" )
5751 parser .add_argument ("--multiplex" , type = str ,
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