Fix nextflow pipeline config lookup

bio-research/skills/nextflow-development/scripts/tests/test_validators.py

@@ -0,0 +1,30 @@
+import sys
+import unittest
+from pathlib import Path
+
+
+SCRIPTS_DIR = Path(__file__).resolve().parents[1]
+sys.path.insert(0, str(SCRIPTS_DIR))
+
+from utils.validators import load_pipeline_config, validate_samplesheet  # noqa: E402
+
+
+class LoadPipelineConfigTest(unittest.TestCase):
+    def test_loads_known_pipeline_config(self):
+        config = load_pipeline_config("rnaseq")
+
+        self.assertIsNotNone(config)
+        self.assertEqual(config["name"], "rnaseq")
+        self.assertIn("samplesheet", config)
+
+    def test_unknown_pipeline_returns_none(self):
+        self.assertIsNone(load_pipeline_config("unknown-pipeline"))
+
+    def test_validate_samplesheet_recognizes_known_pipeline(self):
+        result = validate_samplesheet([], "rnaseq")
+
+        self.assertEqual(result.errors, ["Samplesheet is empty - no samples found"])
+
+
+if __name__ == "__main__":
+    unittest.main()

bio-research/skills/nextflow-development/scripts/utils/validators.py

@@ -44,8 +44,8 @@ def summary(self) -> str:
 def load_pipeline_config(pipeline: str) -> Optional[Dict]:
     """Load pipeline configuration from YAML file."""
     # Find config directory relative to this file
-    script_dir = Path(__file__).parent.parent.parent
-    config_path = script_dir / "config" / "pipelines" / f"{pipeline}.yaml"
+    scripts_dir = Path(__file__).parent.parent
+    config_path = scripts_dir / "config" / "pipelines" / f"{pipeline}.yaml"
 
     if not config_path.exists():
         return None