WIP fix #1330

cwltool/workflow.py

@@ -448,11 +448,12 @@ def job(
             )
 
         step_input = {}
-        for inp in self.tool["inputs"]:
-            field = shortname(inp["id"])
-            if not inp.get("not_connected"):
-                step_input[field] = job_order[inp["id"]]
-
+        for inp in job_order:
+            field = shortname(inp)
+            step_input[field] = job_order[inp]
+            if hasattr(inp, "get"):
+                if not inp.get("not_connected"):
+                    step_input[field] = job_order[field]
         try:
             yield from self.embedded_tool.job(
                 step_input,

cwltool/workflow_job.py

@@ -386,6 +386,9 @@ def object_from_state(
     incomplete: bool = False,
 ) -> Optional[CWLObjectType]:
     inputobj = {}  # type: CWLObjectType
+    for s in state.keys():
+        if hasattr(state[s], "value"):
+            inputobj[s] = state[s].value
     for inp in params:
         iid = original_id = cast(str, inp["id"])
         if frag_only:
@@ -551,6 +554,23 @@ def do_output_callback(self, final_output_callback: OutputCallbackType) -> None:
             _logger.debug("[%s] outputs %s", self.name, json_dumps(wo, indent=4))
 
         self.did_callback = True
+        paramskey = []
+        paramskeys = []
+
+        if self.tool["outputs"] is not None:
+            for inp in self.tool["outputs"]:
+                for k, v in inp.items():
+                    if k == "id":
+                        paramskey.append(v)
+                        paramskeys.append(shortname(v))
+
+        newwo = {}
+        for k, v in wo.items():
+            if k in paramskey:
+                newwo[k] = v
+            elif k in paramskeys:
+                newwo[k] = v
+        wo = newwo
 
         final_output_callback(wo, self.processStatus)