diff --git a/workflow/conf/biohpc.config b/workflow/conf/biohpc.config
index 9f4bf081e96bf6f31b3e1f1d815e86fa7c5dd081..f05eca966aafdf7be4303f3b9147564da6ba2c5e 100644
--- a/workflow/conf/biohpc.config
+++ b/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'
+}
diff --git a/workflow/scripts/map_reads.py b/workflow/scripts/map_reads.py
index 552a2d9735c3c7bf8b4efb3f26b7cd0be0ca1f71..a15cf45c1ae615e8c33fbf4b09ba8213e8349e46 100644
--- a/workflow/scripts/map_reads.py
+++ b/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')