use local file for now; will still fail because of test-setup with mo…

…ck/fakefs etc

snappy_pipeline/base.py

@@ -70,12 +70,9 @@ def expand_ref(config_path, dict_data, lookup_paths=None, dict_class=OrderedDict
     return resolved, tuple(lookup_paths), tuple(config_files)
 
 
-def validate_config(config: dict[Any, Any], workflow: str, file=sys.stderr):
-    print(f"\nValidating config.yaml for {workflow}", file=file)
-    config_schema_path = os.path.join(
-        os.path.dirname(snakefile_path(workflow)), "config.schema.yaml"
-    )
-    validate(config, config_schema_path)
+def validate_config(config: dict[Any, Any], schema_path: str, file=sys.stderr):
+    print(f"\nValidating config.yaml using {schema_path}", file=file)
+    validate(config, schema_path)
 
 
 def print_config(config, file=sys.stderr):

snappy_pipeline/workflows/adapter_trimming/__init__.py

@@ -437,7 +437,8 @@ def __init__(self, parent):
         super().__init__(parent)
         self.base_path_in = "work/input_links/{library_name}"
         self.base_path_out = "work/{trimmer}.{{library_name}}"
-        validate_config({"adapter_trimming": self.config}, "adapter_trimming")
+        schema_path = os.path.abspath(os.path.join(os.path.dirname(__file__), "config.schema.yaml"))
+        validate_config({"adapter_trimming": self.config}, schema_path)
         #: Path generator for linking in
         self.path_gen = LinkInPathGenerator(
             self.parent.work_dir,