fix: copy files if we couldn't move them

Author: psafont

cwltool/process.py

@@ -299,7 +299,8 @@ def _relocate(src, dst):
         if src == dst:
             return
 
-        if action == "move":
+        _action = action
+        if _action == "move":
             # do not move anything if we are trying to move an entity from
             # outside of the source directories
             if any(os.path.commonprefix([path, src]) == path for path in source_directories):
@@ -310,8 +311,11 @@ def _relocate(src, dst):
                         _relocate(dir_entry.path, fs_access.join(dst, dir_entry.name))
                 else:
                     shutil.move(src, dst)
+            else:
+                # we still need the files at the destination, so let's copy them
+                _action = "copy"
 
-        elif action == "copy":
+        if _action == "copy":
             _logger.debug("Copying %s to %s", src, dst)
             if fs_access.isdir(src):
                 if os.path.isdir(dst):