Merge branch 'new_modules' of git.unl.edu:aknecht2/chipathlon into new_modules

chipathlon/workflow.py

@@ -402,6 +402,7 @@ class Workflow(object):
                     os.path.join(self.basepath, "output")
                     )
             # NEED TO DETERMINE HOW TO READ IN THIS INFO
+            sites += """\n\t<profile key="change.dir" namespace="pegasus">true</profile>"""
             for namespace in self.config["profile"]:
                 for key in self.config["profile"][namespace]:
                     sites += """\n\t<profile namespace="%s" key="%s">%s</profile> """ % (namespace, key, self.config["profile"][namespace][key])

chipathlon/workflow_job.py

@@ -188,7 +188,7 @@ class WorkflowJob(object):
                 arg_list.append("%s %s" % (arg, self.params["arguments"][arg] if arg in self.params else arg_info["default"]))
             else:
                 if arg_info["has_value"]:
-                    if arg_info["default"][:1] == "$":
+                    if not isinstance(arg_info["default"], bool) and arg_info["default"][:1] == "$":
                         key, index = arg_info["default"].split(".")
                         arg_list.append(arg)
                         # We only add the file object if the passed argument is
@@ -197,7 +197,7 @@ class WorkflowJob(object):
                     else:
                         arg_list.append("%s %s" % (arg, arg_info["default"]))
                 else:
-                    if arg[:1] == "$":
+                    if not isinstance(arg, bool) and arg[:1] == "$":
                         key, index = arg.split(".")
                         # We only add the file object if the passed argument is
                         # has type == file