Add contextmanager that extends set_wd but changes into a tempdir

nf-core · JulianFlesch · Dec 2, 2025 · Dec 2, 2025 · Dec 2, 2025 · Dec 2, 2025
commit 7c369a420ad40dea0fe759339d4d5895067a6688
diff --git a/nf_core/utils.py b/nf_core/utils.py
@@ -17,6 +17,7 @@
 import shlex
 import subprocess
 import sys
+import tempfile
 import time
 from collections.abc import Callable, Generator
 from contextlib import contextmanager
@@ -1646,6 +1647,17 @@ def set_wd(path: Path) -> Generator[None, None, None]:
         os.chdir(start_wd)
 
 
+@contextmanager
+def set_wd_tempdir() -> Generator[None, None, None]:
+    """
+    Context manager to provide and change into a tempdir and ensure its removal and return to the
+    original_dir upon exceptions.
+    """
+    with tempfile.TemporaryDirectory() as tmp:
+        with set_wd(Path(tmp)):
+            yield
+
+
 def get_wf_files(wf_path: Path):
     """Return a list of all files in a directory (ignores .gitigore files)"""