diff --git a/cwltool/job.py b/cwltool/job.py
index 632174507..bf62577ac 100644
--- a/cwltool/job.py
+++ b/cwltool/job.py
@@ -69,7 +69,8 @@ def run(self, dry_run=False, pull_image=True, rm_container=True, rm_tmpdir=True,
             runtime.append("--read-only=true")
             runtime.append("--net=none")
             euid = docker_vm_uid() or os.geteuid()
-            runtime.append("--user=%s" % (euid))
+            if kwargs.get("no_user") is not True:
+                runtime.append("--user=%s" % (euid))
 
             if rm_container:
                 runtime.append("--rm")
diff --git a/cwltool/main.py b/cwltool/main.py
index 584711e16..542f58ff5 100755
--- a/cwltool/main.py
+++ b/cwltool/main.py
@@ -115,6 +115,7 @@ def arg_parser():
     exgroup.add_argument("--debug", action="store_true", help="Print even more logging")
 
     parser.add_argument("--tool-help", action="store_true", help="Print command line help for tool")
+    parser.add_argument("--no-user", action="store_true", help="Runs container without setting user (default will set user)")
 
     parser.add_argument("workflow", type=str, nargs="?", default=None)
     parser.add_argument("job_order", nargs=argparse.REMAINDER)
@@ -535,6 +536,7 @@ def main(args=None,
                        outdir=args.outdir,
                        tmp_outdir_prefix=args.tmp_outdir_prefix,
                        use_container=args.use_container,
+                       no_user=args.no_user,
                        preserve_environment=args.preserve_environment,
                        pull_image=args.enable_pull,
                        rm_container=args.rm_container,