cwltool: --compute-checksum and --no-compute-checksum are mutually exclusive command line args.

Author: radhika

cwltool/draft2tool.py

@@ -334,6 +334,8 @@ def rm_pending_output_callback(output_callback, jobcachepending,
         else:
             j.command_line = flatten(map(builder.generate_arg, builder.bindings))
 
+        print("******** KWARGS = ", kwargs)
+
         j.pathmapper = builder.pathmapper
         j.collect_outputs = partial(
                 self.collect_output_ports, self.tool["outputs"], builder, compute_checksum=kwargs.get("compute_checksum"))

cwltool/main.py

@@ -158,11 +158,12 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
                         help="Desired workflow behavior when a step fails.  One of 'stop' or 'continue'. "
                         "Default is 'stop.", default="stop")
 
-    parser.add_argument("--compute-checksum", action="store_true", default=True,
+    exgroup = parser.add_mutually_exclusive_group()
+    exgroup.add_argument("--compute-checksum", action="store_true", default=True,
                         help="Compute checksum of contents while collecting outputs",
                         dest="compute_checksum")
-    parser.add_argument("--no-compute-checksum", action="store_false",
-                        help="Compute checksum of contents while collecting outputs",
+    exgroup.add_argument("--no-compute-checksum", action="store_false",
+                        help="Do not compute checksum of contents while collecting outputs",
                         dest="compute_checksum")
 
     parser.add_argument("workflow", type=str, nargs="?", default=None)