Change Workflow.visit() to call WorkflowStep.visit().

Author: Peter Amstutz

cwltool/process.py

@@ -84,7 +84,7 @@ def get_schema():  # type: () -> Tuple[Loader,avro.schema.Names,List[Dict[str,An
 
     return schema_salad.schema.load_schema("https://w3id.org/cwl/CommonWorkflowLanguage.yml", cache=cache)
 
-def get_feature(self, feature):  # type: (Any, Any) -> Tuple[Any, bool] 
+def get_feature(self, feature):  # type: (Any, Any) -> Tuple[Any, bool]
     for t in reversed(self.requirements):
         if t["class"] == feature:
             return (t, True)
@@ -354,7 +354,7 @@ def get_requirement(self, feature):
         return get_feature(self, feature)
 
     def visit(self, op):
-        self.tool = op(self.tool)
+        op(self.tool)
 
     @abc.abstractmethod
     def job(self, job_order, input_basedir, output_callbacks, **kwargs):

cwltool/workflow.py

@@ -398,8 +398,10 @@ def job(self, joborder, basedir, output_callback, **kwargs):
             yield w
 
     def visit(self, op):
-        self.tool = op(self.tool)
-        self.steps = [op(s.tool) for s in self.steps]
+        op(self.tool)
+        for s in self.steps:
+            s.visit(op)
+
 
 class WorkflowStep(Process):
 
@@ -512,6 +514,9 @@ def job(self, joborder, basedir, output_callback, **kwargs):
             _logger.exception("Unexpected exception")
             raise WorkflowException(str(e))
 
+    def visit(self, op):
+        self.embedded_tool.visit(op)
+
 
 class ReceiveScatterOutput(object):