Resolve "Parse ccat / peakranger output into bed files"

Closes #21 (closed), #20 (closed)

Fixed several workflow bugs -- everything is functioning pretty normally now! Results are getting loaded and saved correctly.

chipathlon/jobs/modules/peak_call.yaml

@@ -18,7 +18,7 @@ peak_call:
               type: file
           - peakranger.log:
               type: stdout
-    - sort_awk_sort_peaks:
+    - peakranger_format_bed:
         inputs:
           - region.bed:
               type: file
@@ -26,7 +26,7 @@ peak_call:
         outputs:
           - region_sorted.bed:
               type: file
-    - sort_awk_sort_peaks:
+    - peakranger_format_bed:
         inputs:
           - summit.bed:
               type: file
@@ -51,13 +51,26 @@ peak_call:
         outputs:
           - significant.peak:
               type: file
+              prefix_join: "."
           - significant.region:
               type: file
+              prefix_join: "."
           - top100000.peak:
               type: file
-          - ccat.log:
+              prefix_join: "."
+          - log:
               type: stdout
-    - sort_awk_sort_peaks:
+              prefix_join: "."
+    - ccat_format_bed:
+        inputs:
+          - significant.region:
+              type: file
+        additional_inputs: null
+        outputs:
+          - region_sorted.bed:
+              type: file
+              save_result: true
+    - ccat_format_bed:
         inputs:
           - significant.peak:
               type: file
@@ -117,7 +130,7 @@ peak_call:
               type: file
           - results.ccscore:
               type: file
-    - zcat_awk_sort_peaks:
+    - sort_awk_sort_peaks:
         inputs:
           - results.narrowPeak.gz:
               type: file
@@ -136,7 +149,7 @@ peak_call:
               type: string
         additional_inputs: null
         outputs:
-          - results.narrowPeak:
+          - peaks.narrowPeak:
               type: file
           - results.xls:
               type: file
@@ -144,7 +157,7 @@ peak_call:
               type: file
     - sort_awk_sort_peaks:
         inputs:
-          - results.narrowPeak:
+          - peaks.narrowPeak:
               type: file
         additional_inputs: null
         outputs: