Resolve "Gem output files bug"

Closes #22 (closed)

chipathlon/jobs/modules/peak_call.yaml

@@ -97,10 +97,30 @@ peak_call:
           - chr_fasta:
               type: list
         outputs:
-          - results_sorted.bed:
+          - GEM_events.narrowPeak:
+              type: file
+              name_template: "$prefix$/$prefix$_GEM_events.narrowPeak"
+          - GPS_events.narrowPeak:
+              type: file
+              name_template: "$prefix$/$prefix$_GPS_events.narrowPeak"
+    - sort_awk_sort_peaks:
+        inputs:
+          - GEM_events.narrowPeak:
+              type: file
+        additional_inputs: null
+        outputs:
+          - results_GEM_sorted.bed:
+              type: file
+    - sort_awk_sort_peaks:
+        inputs:
+          - GPS_events.narrowPeak:
+              type: file
+        additional_inputs: null
+        outputs:
+          - results_GPS_sorted.bed:
               type: file
   - spp[tool]:
-    - cp_bed_tagalign:
+    - cp:
         inputs:
           - exp.bed:
               type: file
@@ -108,7 +128,7 @@ peak_call:
         outputs:
           - exp.tagAlign:
               type: file
-    - cp_bed_tagalign:
+    - cp:
         inputs:
           - control.bed:
               type: file