added no-read-only option (#528)

Author: SooLee

cwltool/job.py

@@ -395,7 +395,9 @@ def run(self, pull_image=True, rm_container=True,
             self.add_volumes(self.generatemapper, runtime)
 
         runtime.append(u"--workdir=%s" % (docker_windows_path_adjust(self.builder.outdir)))
-        runtime.append(u"--read-only=true")
+
+        if not kwargs.get("no_read_only"):
+            runtime.append(u"--read-only=true")
 
         if kwargs.get("custom_net", None) is not None:
             runtime.append(u"--net={0}".format(kwargs.get("custom_net")))

cwltool/main.py

@@ -231,6 +231,9 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
     parser.add_argument("--force-docker-pull", action="store_true",
                         default=False, help="Pull latest docker image even if"
                                             " it is locally present", dest="force_docker_pull")
+    parser.add_argument("--no-read-only", action="store_true",
+                        default=False, help="Do not set root directoy in the"
+                                            " container as read-only", dest="no_read_only")
     parser.add_argument("workflow", type=Text, nargs="?", default=None)
     parser.add_argument("job_order", nargs=argparse.REMAINDER)