fix: fix missing storage information when handling already completed …

…checkpoints. This solves a bug causing failure to retrieve storage files in workflows with checkpoints.

snakemake/io.py

@@ -292,7 +292,7 @@ async def inventory(self):
             if self.is_storage and self not in cache.exists_in_storage:
                 # info not yet in inventory, let's discover as much as we can
                 tasks.append(self.storage_object.inventory(cache))
-            if not ON_WINDOWS and self not in cache.exists_local:
+            elif not ON_WINDOWS and self not in cache.exists_local:
                 # we don't want to mess with different path representations on windows
                 tasks.append(self._local_inventory(cache))
             await asyncio.gather(*tasks)
@@ -887,7 +887,7 @@ def is_flagged(value: MaybeAnnotated, flag: str) -> bool:
 
 
 def flag(value, flag_type, flag_value=True):
-    if isinstance(value, AnnotatedString):
+    if isinstance(value, AnnotatedStringInterface):
         value.flags[flag_type] = flag_value
         return value
     if not_iterable(value):

tests/test_checkpoints/Snakefile

@@ -12,7 +12,7 @@ checkpoint somestep:
         "somestep/{sample}.txt"
     shell:
         # simulate some output vale
-        "echo {wildcards.sample} > somestep/{wildcards.sample}.txt"
+        "echo {wildcards.sample} > {output}"
 
 
 rule intermediate: