fix: do not apply module prefix in case of remote files

snakemake/path_modifier.py

@@ -52,11 +52,15 @@ def modify(self, path, property=None):
         return modified_path
 
     def replace_prefix(self, path, property=None):
-        if (
-            self.trie is None and self.prefix is None
-        ) or property in self.skip_properties:
+        if (self.trie is None and self.prefix is None) or (
+            property in self.skip_properties
+            or os.path.isabs(path)
+            or path.startswith("..")
+            or is_flagged(path, "remote_object")
+        ):
             # no replacement
             return path
+
         if self.trie is not None:
             prefixes = self.trie.prefix_items(str(path))
             if len(prefixes) > 1:
@@ -74,10 +78,8 @@ def replace_prefix(self, path, property=None):
             else:
                 # no matching prefix
                 return path
+
         # prefix case
-        if os.path.isabs(path) or path.startswith(".."):
-            # do not apply prefix if path is not within the workdir
-            return path
         return self.prefix + path
 
     def apply_default_remote(self, path):

tests/test_modules_prefix/module-test/Snakefile

@@ -1,13 +1,21 @@
-configfile: "config.yaml" # does not exist, but this statement should be ignored on module import
+from snakemake.remote.HTTP import RemoteProvider as HTTPRemoteProvider
+
+
+configfile: "config.yaml"  # does not exist, but this statement should be ignored on module import
+
+
+HTTP = HTTPRemoteProvider()
 
 
 def some_func():
     return 15
 
 
 rule a:
+    input:
+        HTTP.remote("raw.githubusercontent.com/snakemake/snakemake/main/LICENSE.md"),
     output:
         "results/test.out",
-        "/tmp/foo.txt"
+        "/tmp/foo.txt",
     shell:
-        "echo {config[test]} > {output[0]}; touch {output[1]}"
+        "echo {config[test]} > {output[0]}; touch {output[1]}"