fix use_relative_output_paths when some parent of run dir is a symlink

chanzuckerberg · May 15, 2023 · 8def8d6 · 8def8d6
1 parent d8f0a03
commit 8def8d6
Showing 1 changed file with 3 additions and 1 deletion.
diff --git a/WDL/runtime/task.py b/WDL/runtime/task.py
@@ -920,7 +920,9 @@ def map_path_relative(v: Union[Value.File, Value.Directory]) -> str:
             if path_really_within(target, os.path.join(run_dir, "work")):
                 # target was generated by current task; use its path relative to the task work dir
                 if not os.path.basename(run_dir).startswith("download-"):  # except download tasks
-                    rel_link = os.path.relpath(real_target, os.path.join(run_dir, "work"))
+                    rel_link = os.path.relpath(
+                        real_target, os.path.realpath(os.path.join(run_dir, "work"))
+                    )
             else:
                 # target is an out/ link generated by a call in the current workflow OR a cached
                 # run; use the link's path relative to that out/ dir, which by induction should