Added more debug statements and fixed file_list parsing in workflow_job.

chipathlon/workflow_job.py

@@ -512,16 +512,13 @@ class WorkflowJob(object):
         passed in.
         """
         arg_value = self._get_arg_value(arg_name, arg_info)
+        if self.debug:
+            print "arg_value: %s" % (arg_value,),
         add_value = arg_value
         if (isinstance(arg_value, str) and arg_value.startswith("$")) or arg_info["type"] == "rawfile":
             arg_value = arg_value[1:]
             if arg_info["type"] == "rawfile":
                 add_value = self.raw_files[os.path.basename(arg_value)]["file"]
-            elif arg_info["type"] == "file_list":
-                # Lists can only be loaded from inputs
-                add_value = []
-                for file_dict in inputs[arg_value]["values"]:
-                    add_value.append(file_dict["file"].name)
             else:
                 # Conditionally load from inputs / outputs
                 # This will only load the dict of information though, not
@@ -538,6 +535,11 @@ class WorkflowJob(object):
         elif arg_info["type"] == "rawfolder":
             # We want just the folder name
             add_value = os.path.basename(os.path.dirname(arg_value + "/"))
+        elif arg_info["type"] == "file_list":
+            add_value = []
+            for val in arg_value:
+                file_name = val[1:]
+                add_value.append((inputs if file_name in inputs else outputs)[file_name]["file"].name)
         return add_value
 
     def _create_arg_list(self, inputs, outputs):
@@ -567,8 +569,10 @@ class WorkflowJob(object):
             # 1. Should we add the argument name?
             # 2. What's the correct value to add?
             if self.debug:
-                print "\t%s: Loading argument: %s, info: %s" % (self, arg_name, arg_info)
+                print "\t%s: Loading argument: %s, info: %s, " % (self, arg_name, arg_info),
             add_value = self._interpolate_value(inputs, outputs, arg_name, arg_info)
+            if self.debug:
+                print "Final value: %s" % (add_value)
             # Only add arguments that have a value
             if add_value is not None:
                 # Need to add in the arg_name and the arg_value