Updated 3 things: 1st changed pepr arguments to be a list with a separator. ...

Updated 3 things: 1st changed pepr arguments to be a list with a separator.  Updated argument parsing to allow joining list arguments with another value.  Updated conf to allow separator as a valid argument option.

chipathlon/conf.py

@@ -120,7 +120,7 @@ argument_types = {
 # Defines information about arguments
 argument_keys = {
     "required": ["type", "changeable", "has_value"],
-    "optional": ["required", "default", "file_type", "path"]
+    "optional": ["required", "default", "file_type", "path", "separator"]
 }
 
 # workflow_job keys

chipathlon/jobs/params/pepr_callpeak.yaml

@@ -20,17 +20,23 @@ pepr_callpeak:
   command: pepr
   arguments:
     - "-c":
-        type: file
+        type: list
+        separator: ","
         changeable: false
         required: true
         has_value: true
-        default: "$inputs.0,$inputs.0"
+        default:
+          - $inputs.0
+          - $inputs.0
     - "-i":
-        type: file
+        type: list
+        separator: ","
         changeable: false
         required: true
         has_value: true
-        default: "$inputs.1,$inputs.1"
+        default:
+          - $inputs.1
+          - $inputs.1
     - "-n":
         type: string
         changeable: true

chipathlon/workflow_job.py

@@ -514,9 +514,12 @@ class WorkflowJob(object):
                     arg_list.append(arg_name)
                     arg_list.append(add_value)
                 elif isinstance(add_value, list):
-                    arg_list.append(arg_name)
-                    for f in add_value:
-                        arg_list.append(f)
+                    if "separator" in arg_info:
+                        arg_list.append(arg_info["seperator"].join(add_value))
+                    else:
+                        arg_list.append(arg_name)
+                        for f in add_value:
+                            arg_list.append(f)
                 else:
                     arg_list.append("%s %s" % (arg_name, add_value))
             else: