PePr updates

chipathlon/generators/peak_call_generator.py

@@ -32,7 +32,7 @@ class PeakCallGenerator(ModuleGenerator):
             "peakranger": self._peakranger,
             "zerone": self._zerone,
             "hiddendomains": self._hiddendomains,
-            "pepr": self._hiddendomains
+            "pepr": self._pepr
         }
         self.call_pairs = {}
         if debug:
@@ -170,7 +170,9 @@ class PeakCallGenerator(ModuleGenerator):
         call_pair = self.call_pairs[result.full_name]
         inputs = {
             "control.bed": call_pair[0].full_name,
-            "signal.bed": call_pair[1].full_name
+            "signal.bed": call_pair[1].full_name,
+            "prefix": result.prefix,
+            "peak_type": run.peak_type
         }
         additional_inputs = {}
         return (self.get_markers(run), inputs, additional_inputs)

chipathlon/jobs/modules/peak_call.yaml

@@ -308,19 +308,20 @@ peak_call:
                 type: file
                 final_result: true
   - pepr[tool]:
-    - broad[peak_type]:
-      - pepr_callpeak:
-          inputs:
-            - control.bed:
-                type: file
-            - signal.bed:
-                type: file
-          additional_inputs: null
-          outputs:
-            - pepr_result.bed:
-                type: file
-                final_result: true
-            - pepr_parameters.txt:
-                type: file
-            - pepr_log.txt:
-                type: file
+    - pepr_callpeak:
+        inputs:
+          - control.bed:
+              type: file
+          - signal.bed:
+              type: file
+          - prefix:
+              type: string
+          - peak_type:
+              type: string
+        additional_inputs: null
+        outputs:
+          - pepr_result.bed:
+              type: file
+              final_result: true
+          - pepr_parameters.txt:
+              type: file

chipathlon/jobs/params/pepr_callpeak.yaml

@@ -6,6 +6,10 @@ pepr_callpeak:
     - name: signal
       type: file
       file_type: bed
+    - name: prefix
+      type: string
+    - name: peak_type
+      type: string
   additional_inputs: null
   outputs:
     - name: pepr_result
@@ -14,9 +18,6 @@ pepr_callpeak:
     - name: pepr_parameters
       type: file
       file_type: txt
-    - name: pepr_log
-      type: file
-      file_type: txt
   command: pepr
   arguments:
     - "-c":
@@ -38,11 +39,11 @@ pepr_callpeak:
           - $inputs.1
           - $inputs.1
     - "-n":
-        type: string
+        type: file
         changeable: true
-        required: false
+        required: true
         has_value: true
-        default: "NA"
+        default: $inputs.2
     - "-f":
         type: string
         changeable: true
@@ -62,9 +63,9 @@ pepr_callpeak:
         has_value: true
         default: 100
     - "--diff":
-        type: boolean
-        changeable: true
-        required: false
+        type: string
+        changeable: false
+        required: true
         has_value: false
     - "--threshold":
         type: string
@@ -77,7 +78,7 @@ pepr_callpeak:
         changeable: true
         required: true
         has_value: true
-        default: "broad"
+        default: "$inputs.3"
     - "--normalization":
         type: string
         changeable: true

chipathlon/run_parser.py

@@ -25,7 +25,7 @@ class RunParser(object):
                 self.yaml_data = yaml.load(rh)
                 self._load_runs(mdb)
             except yaml.YAMLError as e:
-                self.err += "Error parsing run template file [%s]: %s.\n" % (self.run_file, e)
+                self.errors.append("Error parsing run template file [%s]: %s.\n" % (self.run_file, e))
         return
 
     def is_valid(self):

chipathlon/workflow_job.py

@@ -514,14 +514,13 @@ class WorkflowJob(object):
                     arg_list.append(arg_name)
                     arg_list.append(add_value)
                 elif isinstance(add_value, list):
-                    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)
+                    arg_list.append(arg_name)
+                    for i,f in enumerates(add_value):
+                        arg_list.append(f)
+                        if "separator" in arg_info and i != len(add_value) - 1:
+                            arg_list.append(arg_info["separator"])    
                 else:
                     arg_list.append("%s %s" % (arg_name, add_value))
             else:
                 arg_list.append(add_value)
-        return arg_list
+        return arg_list
\ No newline at end of file