diff --git a/cwltool/docker.py b/cwltool/docker.py
index 7e7c93507..62b83ca9a 100644
--- a/cwltool/docker.py
+++ b/cwltool/docker.py
@@ -236,7 +236,7 @@ def add_file_or_directory_volume(
         """Append volume a file/dir mapping to the runtime option list."""
         if not volume.resolved.startswith("_:"):
             _check_docker_machine_path(volume.resolved)
-            self.append_volume(runtime, volume.resolved, volume.target)
+            self.append_volume(runtime, volume.resolved, volume.target, writable=volume.staged)
 
     def add_writable_file_volume(
         self,
diff --git a/cwltool/job.py b/cwltool/job.py
index 4011641cd..bc926d533 100644
--- a/cwltool/job.py
+++ b/cwltool/job.py
@@ -100,12 +100,23 @@ def relink_initialworkdir(
                 continue
             host_outdir_tgt = os.path.join(host_outdir, vol.target[len(container_outdir) + 1 :])
             if os.path.islink(host_outdir_tgt) or os.path.isfile(host_outdir_tgt):
+                try:
+                    ensure_writable(host_outdir_tgt, include_root=True)
+                except PermissionError:
+                    pass
                 try:
                     os.remove(host_outdir_tgt)
                 except PermissionError:
                     pass
             elif os.path.isdir(host_outdir_tgt) and not vol.resolved.startswith("_:"):
-                shutil.rmtree(host_outdir_tgt)
+                try:
+                    ensure_writable(host_outdir_tgt, include_root=True)
+                except PermissionError:
+                    pass
+                try:
+                    shutil.rmtree(host_outdir_tgt)
+                except PermissionError:
+                    pass
             if not vol.resolved.startswith("_:"):
                 try:
                     os.symlink(vol.resolved, host_outdir_tgt)