Fail workflows with separate flag without prefix

Author: Anton Khodak

cwltool/builder.py

@@ -212,6 +212,9 @@ def generate_arg(self, binding):  # type: (Dict[Text,Any]) -> List[Text]
 
         prefix = binding.get("prefix")
         sep = binding.get("separate", True)
+        if prefix is None and not sep:
+            with SourceLine(binding, "separate", WorkflowException, _logger.isEnabledFor(logging.DEBUG)):
+                raise WorkflowException("'separate' option can not be specified without prefix")
 
         l = []  # type: List[Dict[Text,Text]]
         if isinstance(value, list):
@@ -240,7 +243,7 @@ def generate_arg(self, binding):  # type: (Dict[Text,Any]) -> List[Text]
             if sep:
                 args.extend([prefix, self.tostr(j)])
             else:
-                args.append((prefix or "") + self.tostr(j))
+                args.append(prefix + self.tostr(j))
 
         return [a for a in args if a is not None]
 

tests/test_examples.py

@@ -7,6 +7,7 @@
 
 from io import StringIO
 
+from cwltool.errors import WorkflowException
 from cwltool.utils import onWindows
 
 try:
@@ -522,10 +523,11 @@ def test_malformed_outputs(self):
             echo()
 
     def test_separate_without_prefix(self):
-        # check that setting 'separate = false' on an inputBinding without prefix does not fail the workflow
-        f = cwltool.factory.Factory()
-        echo = f.make(get_data("tests/wf/separate_without_prefix.cwl"))
-        self.assertEqual(echo(), {"output": "string\n"})
+        # check that setting 'separate = false' on an inputBinding without prefix fails the workflow
+        with self.assertRaises(WorkflowException):
+            f = cwltool.factory.Factory()
+            echo = f.make(get_data("tests/wf/separate_without_prefix.cwl"))
+            echo()
 
 
     def test_checker(self):