Resolve "Add in Macs2 support"

Closes #7 (closed) and adds in naive overlap of peaks

workflow/conf/biohpc.config

@@ -37,21 +37,41 @@ process {
   }
   $poolAndPsuedoReads {
     module = ['python/3.6.1-2-anaconda']
+    executor = 'local'
+  }
+  $callPeaksMACS {
+    module = ['python/3.6.1-2-anaconda', 'phantompeakqualtools/1.2', 'macs/2.1.0-20151222', 'UCSC_userApps/v317', 'bedtools/2.26.0']
     cpus = 32
   }
+  $consensusPeaks {
+    module = ['python/3.6.1-2-anaconda', 'bedtools/2.26.0']
+    cpus = local
+  }
 }
 
 params {
   // Reference file paths on BioHPC
   genomes {
-    'GRCh38' { bwa = '/project/shared/bicf_workflow_ref/GRCh38' }
-    'GRCh37' { bwa = '/project/shared/bicf_workflow_ref/GRCh37' }
-    'GRCm38' { bwa = '/project/shared/bicf_workflow_ref/GRCm38' }
+    'GRCh38' {
+      bwa = '/project/shared/bicf_workflow_ref/GRCh38'
+      genomesize = 'hs'
+      chromsizes = '/project/shared/bicf_workflow_ref/GRCh38/genomefile.txt'
+    }
+    'GRCh37' {
+      bwa = '/project/shared/bicf_workflow_ref/GRCh37'
+      genomesize = 'hs'
+      chromsizes = '/project/shared/bicf_workflow_ref/GRCh37/genomefile.txt'
+    }
+    'GRCm38' {
+      bwa = '/project/shared/bicf_workflow_ref/GRCm38'
+      genomesize = 'mm'
+      chromsizes = '/project/shared/bicf_workflow_ref/GRCm38/genomefile.txt'
+    }
   }
 }
 
 trace {
-    enabled = true
-    file = 'pipeline_trace.txt'
-    fields = 'task_id,native_id,process,name,status,exit,submit,start,complete,duration,realtime,%cpu,%mem,rss'
+  enabled = true
+  file = 'pipeline_trace.txt'
+  fields = 'task_id,native_id,process,name,status,exit,submit,start,complete,duration,realtime,%cpu,%mem,rss'
 }