Commit acdc8601 authored by aknecht2's avatar aknecht2
Browse files

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

parents f59d8b25 de3e6ff1
......@@ -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])
......
......@@ -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
......
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