writable directories w/o inplace update get copied to the host target, not the in_container path (#756)

Author: mr-c

cwltool/command_line_tool.py

@@ -276,6 +276,7 @@ def job(self,
 
             if dockerimg:
                 cmdline = ["docker", "run", dockerimg] + cmdline
+                # not really run using docker, just for hashing purposes
             keydict = {u"cmdline": cmdline}
 
             if "stdout" in self.tool:

cwltool/singularity.py

@@ -194,7 +194,7 @@ def add_volumes(self, pathmapper, runtime, stage_output):
                             docker_windows_path_adjust(vol.resolved),
                             docker_windows_path_adjust(containertgt)))
                     else:
-                        shutil.copytree(vol.resolved, vol.target)
+                        shutil.copytree(vol.resolved, host_outdir_tgt)
             elif vol.type == "CreateFile":
                 createtmp = os.path.join(host_outdir, os.path.basename(vol.target))
                 with open(createtmp, "wb") as tmp: