From 0205044c94f0956e18a3ac9df07dbf1de5ac2eec Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Fri, 6 Oct 2017 13:15:14 -0500
Subject: [PATCH] Add in trace config and fix varaible of map_reads.
---
workflow/conf/biohpc.config | 6 ++++++
workflow/scripts/map_reads.py | 1 +
2 files changed, 7 insertions(+)
diff --git a/workflow/conf/biohpc.config b/workflow/conf/biohpc.config
index 9f4bf08..f05eca9 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 552a2d9..a15cf45 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')
--
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