Fixed issues with ccat output files.

chipathlon/jobs/modules/peak_call.yaml

@@ -49,25 +49,30 @@ peak_call:
               type: string
         additional_inputs: null
         outputs:
-          - ccat.significant.peak:
+          - significant.peak:
               type: file
-          - ccat.significant.region:
+              prefix_join: "."
+          - significant.region:
               type: file
-          - ccat.top100000.peak:
+              prefix_join: "."
+          - top100000.peak:
               type: file
-          - ccat.log:
+              prefix_join: "."
+          - log:
               type: stdout
+              prefix_join: "."
     - ccat_format_bed:
         inputs:
-          - ccat.significant.region:
+          - significant.region:
               type: file
         additional_inputs: null
         outputs:
           - region_sorted.bed:
               type: file
+              save_result: true
     - ccat_format_bed:
         inputs:
-          - ccat.significant.peak:
+          - significant.peak:
               type: file
         additional_inputs: null
         outputs:

chipathlon/peak_call_generator.py

@@ -70,7 +70,7 @@ class PeakCallGenerator(ModuleGenerator):
             # The prefix mod is because ccat files have double extensions,
             # and we can't control the names of the output files directly,
             # only with the prefix.
-            "prefix": "_".join(result.prefix.split("_")[:-1])
+            "prefix": result.prefix
         }
         additional_inputs = {}
         return (markers, inputs, additional_inputs)