Add staging of gem read distribution file

chipathlon/conf.py

@@ -52,7 +52,8 @@ file_extensions = {
     "yaml": ["yaml"],
     "result": ["bed", "narrowPeak", "broadPeak", "tagAlign", "bam"],
     "txt": ["txt"],
-    "chrom_sizes": ["sizes"]
+    "chrom_sizes": ["sizes"],
+    "read_dist" : ["txt"]
 }
 
 # list of resources that can be specified per job (step) in

chipathlon/jobs/modules/peak_call.yaml

@@ -10,7 +10,9 @@ peak_call:
               type: file
           - prefix:
               type: string
-        additional_inputs: null
+        additional_inputs:
+          - read.dist:
+              type: file
         outputs:
           - results_sorted.narrowPeak:
               type: file

chipathlon/jobs/params/gem_callpeak.yaml

@@ -8,7 +8,9 @@ gem_callpeak:
         type: file
     - prefix:
         type: argument
-  additional_inputs: null
+  additional_inputs:
+    - read_dist:
+        type: file
   outputs:
     - bed:
         type: file

chipathlon/peak_call_generator.py

@@ -44,7 +44,9 @@ class PeakCallGenerator(ModuleGenerator):
             "control.bed": file_pair[1]["file_name"],
             "prefix": prefix
         }
-        additional_inputs = {}
+        additional_inputs = {
+            "read.dist" : self.module.workflow_jobs['gem_callpeak'].raw_files.keys()[0]
+        }
         sample_data = [file_pair[0]["sample"], file_pair[1]["sample"]]
         experiment_ids = file_pair[0]["experiment_ids"]
         control_ids = file_pair[1]["control_ids"]