Update doc

README.md

@@ -199,7 +199,8 @@ Optional arguments:
 `-n`: dry run: show which rules will be launched without run anything.  
 `--cluster-config`: erase the default cluster config file (see above) with a new one.  
 `-c`: clean after launch: keep only filtered results.  
-`--out-step`: specify the output rule file to only run the workflow until the associated rule (run all workflow if not specified)
+`--out-step`: specify the output rule file to only run the workflow until the associated rule (run all workflow if not specified)  
+`--chromosomes CHRS`: list of chromosomes to study, coma separated. Default: all chromosomes of the reference
 
 ### Rerun a workflow
 

cnvpipelines.py

@@ -385,10 +385,10 @@ if __name__ == "__main__":
                             nargs="+", choices=TOOLS)
     detection_parser.add_argument('-s', '--samples', type=str, required=True, help="File containing all samples")
     add_run_and_rerun_options(detection_parser)
-    detection_parser.add_argument('-w', '--wdir', type=str, required=True,
-                           help="Output folder where data will be stored")
     detection_parser.add_argument('--chromosomes', type=str, required=False,
                                   help="List of chromosomes to study, coma separated [default: all]")
+    detection_parser.add_argument('-w', '--wdir', type=str, required=True,
+                           help="Output folder where data will be stored")
     detection_parser.set_defaults(func="run_detection")
 
     # ---Reference bundle: