Add in trace config and fix varaible of map_reads.

workflow/conf/biohpc.config

@@ -25,3 +25,9 @@ params {
     'GRCm38' { bwa = '/project/shared/bicf_workflow_ref/GRCm38' }
   }
 }
+
+trace {
+    enabled = true
+    file = 'pipeline_trace.txt'
+    fields = 'task_id,native_id,process,name,status,exit,submit,start,complete,duration,realtime,%cpu,%mem,rss'
+}

workflow/scripts/map_reads.py

@@ -159,6 +159,7 @@ def align_pe(fastq, sai, reference, fastq_basename):
 
 def main():
     args = get_args()
+    paired = args.paired
 
     # Create a file handler
     handler = logging.FileHandler('map.log')