attempt to properly deal with multiextValue under apply_wildcards & apply_default_storage

WardDeb · WardDeb · commit 4bc0bf202ffb · 2025-03-12T23:02:51.000+01:00
diff --git a/snakemake/io.py b/snakemake/io.py
@@ -1090,6 +1090,8 @@ def format_match(match):
         except KeyError as ex:
             raise WildcardError(str(ex))
 
+    if isinstance(pattern, MultiextValue):
+        return WILDCARD_REGEX.sub(format_match, pattern.prefix)
     return WILDCARD_REGEX.sub(format_match, pattern)
 
 
diff --git a/snakemake/path_modifier.py b/snakemake/path_modifier.py
@@ -117,7 +117,6 @@ def is_annotated_callable(value):
             or is_flagged(path, "storage_object")
             or is_flagged(path, "local")
             or is_flagged(path, "sourcecache_entry")
-            or is_flagged(path, "multiext")
             or is_annotated_callable(path)
         ):
             # no default remote needed
@@ -127,7 +126,10 @@ def is_annotated_callable(value):
         prefix = self.workflow.storage_settings.default_storage_prefix
         if prefix and not prefix.endswith("/"):
             prefix = f"{prefix}/"
-        query = f"{prefix}{os.path.normpath(path)}"
+        if isinstance(path, MultiextValue):
+            query = f"{prefix}{os.path.normpath(path.prefix)}"
+        else:
+            query = f"{prefix}{os.path.normpath(path)}"
         storage_object = self.workflow.storage_registry.default_storage_provider.object(
             query
         )
