Fixed stdout & stderr type handling. Fixed incorrect type in align.yaml. Fixed typo in config.

chipathlon/conf.py

@@ -51,7 +51,7 @@ resources = {
 argument_types = {
     "argument": ["argument"],
     "file": ["file", "stdout", "stderr"]
-]
+}
 
 # param keys
 param_keys = {

chipathlon/jobs/modules/align.yaml

@@ -91,7 +91,7 @@ align:
                     type: file
             outputs:
               - align.sam:
-                  type: stdout
+                  type: file
               - align.quality:
                   type: stderr
       paired[read_end]:
@@ -120,7 +120,7 @@ align:
                   type: file
             outputs:
               - align.sam:
-                  type: stdout
+                  type: file
               - align.quality:
                   type: stderr
   - samtools_sam_to_bam:

chipathlon/workflow_job.py

@@ -197,16 +197,30 @@ class WorkflowJob(object):
                         key, index = arg_info["default"].split(".")
                         arg_list.append(arg)
                         # We only add the file object if the passed argument is
-                        # has type == file
-                        arg_list.append(argument_map[key][int(index)]["file"] if argument_map[key][int(index)]["type"] == "file" else argument_map[key][int(index)]["value"])
+                        # has type == file.  We don't want to process
+                        # stdout / stderr arguments here.
+                        if argument_map[key][int(index)]["type"] == "file":
+                            arg_list.append(argument_map[key][int(index)]["file"])
+                        elif argument_map[key][int(index)]["type"] == "argument":
+                            arg_list.append(argument_map[key][int(index)]["value"])
+                        else:
+                            print "Error with argument '%s' for file %s.  Check the yaml file." % (arg, self.jobname)
+                            sys.exit(1)
                     else:
                         arg_list.append("%s %s" % (arg, arg_info["default"]))
                 else:
                     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
-                        arg_list.append(argument_map[key][int(index)]["file"] if argument_map[key][int(index)]["type"] == "file" else argument_map[key][int(index)]["value"])
+                        # We only add the file object if the passed argument
+                        # has type == file.  We don't want to process
+                        # stdout / stderr arguments here.
+                        if argument_map[key][int(index)]["type"] == "file":
+                            arg_list.append(argument_map[key][int(index)]["file"])
+                        elif argument_map[key][int(index)]["type"] == "argument":
+                            arg_list.append(argument_map[key][int(index)]["value"])
+                        else:
+                            print "Error with argument '%s' for file %s.  Check the yaml file." % (arg, self.jobname)
+                            sys.exit(1)
                     else:
                         arg_list.append(arg)
         return arg_list

chipathlon/workflow_module.py

@@ -131,7 +131,7 @@ class WorkflowModule(object):
                         param_name = param_dict.keys()[0]
                         param = param_dict[param_name]
                         # Make sure param is one of the file types
-                        if param["type"] in conf.argument_types["file"]:
+                        if param["type"] in chipathlon.conf.argument_types["file"]:
                             if param_name not in [x["name"] for x in param_list] and param_name not in [x["name"] for x in output_files]:
                                 if prefix is None or self._get_full_name(prefix, markers, param_name) not in master_files:
                                     param_list.append({"name": param_name, "type": "file"})
@@ -172,7 +172,7 @@ class WorkflowModule(object):
             for job_dict in job_info[param_type]:
                 param_name = job_dict.keys()[0]
                 param = job_dict[param_name]
-                if param["type"] in conf.argument_types["file"]:
+                if param["type"] in chipathlon.conf.argument_types["file"]:
                     full_name = self._get_full_name(prefix, markers, param_name)
                     # If file is an output file, add to master_files
                     if param_type == "outputs":
@@ -233,7 +233,7 @@ class WorkflowModule(object):
             }
             data = module_params
             for arg_params, param_key in zip([inputs, additional_files], ["inputs", "additional_files"]):
-                for file_dict in [file_param for file_param in module_params[param_key] if file_param["type"] in conf.argument_types["file"]]:
+                for file_dict in [file_param for file_param in module_params[param_key] if file_param["type"] in chipathlon.conf.argument_types["file"]]:
                     file_name = file_dict["name"]
                     if file_name not in module_params[param_key]:
                         valid_params = False
@@ -242,7 +242,7 @@ class WorkflowModule(object):
                         valid_params = False
                         msg += "Error loading '%s' jobs.  File with name '%s', value '%s', does not exist in master_files.\n" % (self.name, file_name, arg_params[file_name])
                 for param_dict in module_params[param_key]:
-                    if param_dict["type"] in conf.argument_types["file"]:
+                    if param_dict["type"] in chipathlon.conf.argument_types["file"]:
                         file_name = param_dict["name"]
                         if file_name not in arg_params:
                             valid_params = False