Fixed arguments for pepr peak calling. Updated params in peak_call module to...

Fixed arguments for pepr peak calling.  Updated params in peak_call module to correctly reflect the output files produced by hidden domains.

chipathlon/jobs/modules/peak_call.yaml

@@ -339,7 +339,7 @@ peak_call:
             prefix:
               param_name: prefix
           outputs:
-            result.bed:
+            analysis.bed:
               param_name: result_peaks
             vis.bed:
               param_name: enriched_bins
@@ -351,7 +351,7 @@ peak_call:
               param_name: treatment_bins
       - hiddendomains_format:
           inputs:
-            result.bed:
+            analysis.bed:
               param_name: result_peaks
           outputs:
             results_sorted.bed:

chipathlon/jobs/params/pepr_callpeak.yaml

@@ -20,7 +20,7 @@ pepr_callpeak:
   command: PePr
   arguments:
     - "-c":
-        type: list
+        type: file_list
         separator: ","
         changeable: false
         required: true
@@ -29,7 +29,7 @@ pepr_callpeak:
           - $control.bed
           - $control.bed
     - "-i":
-        type: list
+        type: file_list
         separator: ","
         changeable: false
         required: true
@@ -54,18 +54,11 @@ pepr_callpeak:
         changeable: true
         required: false
         has_value: true
-        default: 10
     - "-w":
         type: numeric
         changeable: true
         required: false
         has_value: true
-        default: 100
-    - "--diff":
-        type: string
-        changeable: false
-        required: true
-        has_value: false
     - "--threshold":
         type: string
         changeable: true
@@ -89,7 +82,6 @@ pepr_callpeak:
         changeable: true
         required: false
         has_value: true
-        default: 10000000
     - "--num-processors":
         type: numeric
         changeable: true