Updated pepr yaml files to copy duplicate control / signal files under new name.

chipathlon/jobs/modules/peak_call.yaml

@@ -358,12 +358,30 @@ peak_call:
               param_name: full_result
               final_result: true
   - pepr[tool]:
+    - cp:
+        inputs:
+          control.bed:
+            param_name: input_file
+        outputs:
+          control2.bed:
+            param_name: output_file
+    - cp:
+        inputs:
+          signal.bed:
+            param_name: input_file
+        outputs:
+          signal2.bed:
+            param_name: output_file
     - pepr_callpeak:
         inputs:
           control.bed:
-            param_name: control.bed
+            param_name: control1.bed
+          control2.bed:
+            param_name: control2.bed
           signal.bed:
-            param_name: signal.bed
+            param_name: signal1.bed
+          signal2.bed:
+            param_name: signal2.bed
           prefix:
             param_name: prefix
           peak_type:

chipathlon/jobs/params/pepr_callpeak.yaml

 pepr_callpeak:
   inputs:
-    control.bed:
+    control1.bed:
       type: file
       file_type: bed
-    signal.bed:
+    control2.bed:
+      type: file
+      file_type: bed
+    signal1.bed:
+      type: file
+      file_type: bed
+    signal2.bed:
       type: file
       file_type: bed
     prefix:
@@ -26,8 +32,8 @@ pepr_callpeak:
         required: true
         has_value: true
         default:
-          - $control.bed
-          - $control.bed
+          - $control1.bed
+          - $control2.bed
     - "-i":
         type: file_list
         separator: ","
@@ -35,8 +41,8 @@ pepr_callpeak:
         required: true
         has_value: true
         default:
-          - $signal.bed
-          - $signal.bed
+          - $signal1.bed
+          - $signal2.bed
     - "-n":
         type: string
         changeable: true