Fixed peak calling workflow generation, updated configuration and yaml files.

chipathlon/conf.py

@@ -21,7 +21,9 @@ file_extensions = {
     "bwa_genome": ["amb", "ann", "bwt", "pac", "sa"],
     "bowtie2_genome": ["1.bt2", "2.bt2", "3.bt2", "4.bt2", "rev.1.bt2", "rev.2.bt2"],
     "quality": ["quality"],
-    "qc": ["qc"]
+    "qc": ["qc"],
+    "pdf": ["pdf"],
+    "ccscore": ["ccscore"]
 }
 
 # list of resources that can be specified per job (step) in

chipathlon/jobs/params/macs2_callpeak.yaml

@@ -6,6 +6,7 @@ macs2_callpeak:
         type: file
     - prefix:
         type: argument
+  additional_inputs: null
   outputs:
     - bed:
         type: file

chipathlon/jobs/params/r_spp_nodups.yaml

@@ -4,6 +4,7 @@ r_spp_nodups:
         type: file
     - bam:
         type: file
+  additional_inputs: null
   outputs:
     - bed:
         type: file
@@ -42,17 +43,17 @@ r_spp_nodups:
         changeable: false
         required: true
         has_value: true
-        default: $outputs.1
+        default: $outputs.0
     - "-savp":
         changeable: false
         required: true
         has_value: true
-        default: $outputs.2
+        default: $outputs.1
     - "-out":
         changeable: false
         required: true
         has_value: true
-        default: $outputs.3
+        default: $outputs.2
     - "-fdr":
         changeable: true
         required: false

chipathlon/jobs/params/sort_awk_sort_peaks.yaml

@@ -2,6 +2,7 @@ sort_awk_sort_peaks:
   inputs:
     - bed:
         type: file
+  additional_inputs: null
   outputs:
     - bed:
         type: file

chipathlon/jobs/params/zcat_awk_sort_peaks.yaml

@@ -2,6 +2,7 @@ zcat_awk_sort_peaks:
   inputs:
     - bed:
         type: file
+  additional_inputs: null
   outputs:
     - bed:
         type: file

chipathlon/workflow.py

@@ -58,6 +58,7 @@ class Workflow(object):
             self._add_download()
             self._add_align()
             self._add_remove_duplicates()
+            self._add_peak_calling()
             # Create pegasus important stuff
             self._create_setup()
             self._add_notify()
@@ -334,11 +335,9 @@ class Workflow(object):
                 # prefix and add in as input_files
                 # remove_duplicates returns prefix_no_dups.bam
                 # REMEMBER: experiment is always first
-                final_prefix = ""
-                for i, file_tuple in enumerate(pair):
-                    prefix = run["prefix"][i]
-                    inputs["exp.bam"] = prefix + "_no_dups.bam"
-                    final_prefix += prefix
+                final_prefix = run["prefix"][0] + "_" + run["prefix"][1]
+                inputs["exp.bam"] = run["prefix"][0] + "_no_dups.bam"
+                inputs["control.bam"] = run["prefix"][1] + "_no_dups.bam"
                 if run["peak"] == "spp":
                     pass
                 elif run["peak"] == "macs2":