fix: parsing snappy config for with WGS projects (#231)

cubi_tk/snappy/itransfer_sv_calling.py

@@ -15,16 +15,15 @@
 
 
 class SnappyStepNotFoundException(Exception):
-    def __str__(self):
-        return "snappy-pipeline config does not define the expected steps this function needs."
+    """Raise when snappy-pipeline config does not define the expected steps this function needs."""
 
 
 class SnappyItransferSvCallingCommand(IndexLibrariesOnlyMixin, SnappyItransferCommandBase):
     """Implementation of snappy itransfer command for variant calling results."""
 
     fix_md5_files = True
     command_name = "itransfer-sv-calling"
-    step_names = ("sv_calling", "sv_calling_targeted")
+    step_names = ("sv_calling_wgs", "sv_calling_targeted")
     start_batch_in_family = True
 
     def __init__(self, args):
@@ -46,7 +45,15 @@ def __init__(self, args):
                 f"Could not find any sv-calling step name in 'config.yaml'. Was looking for one of: {', '.join(self.__class__.step_names)}"
             )
 
-        self.defined_callers = config["step_config"][self.step_name]["tools"]
+        if self.step_name == "sv_calling_targeted":
+            self.defined_callers = config["step_config"][self.step_name]["tools"]
+        else:  # if self.step_name == 'sv_calling_wgs'
+            # For WGS config looks like: sv_calling_wgs::tools::<dna>::[...]
+            self.defined_callers = [
+                tool
+                for subcat in config["step_config"][self.step_name]["tools"]
+                for tool in config["step_config"][self.step_name]["tools"][subcat]
+            ]
 
     @classmethod
     def setup_argparse(cls, parser: argparse.ArgumentParser) -> None:

tests/test_snappy_itransfer_sv_calling.py

@@ -42,10 +42,11 @@ def fake_config(n_tools=1):
 
     tool2 = textwrap.dedent(
         r"""
-          sv_calling:
-            tools:
-              - gcnv
-              - manta
+          sv_calling_wgs:
+            dna:
+              tools:
+                - gcnv
+                - manta
         dummy_line
         """
     ).rstrip("dummy_line\n")