From 5b792c557dd55412dc63139c8daaa7c78c639150 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Wed, 18 Oct 2017 06:52:53 -0500
Subject: [PATCH] Fix params.
---
workflow/scripts/map_qc.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/workflow/scripts/map_qc.py b/workflow/scripts/map_qc.py
index db9973c..e33035f 100644
--- a/workflow/scripts/map_qc.py
+++ b/workflow/scripts/map_qc.py
@@ -159,7 +159,7 @@ def dedup_mapped(bam, bam_basename, paired):
with open(dup_file_qc_filename, 'w') as fh:
sambamba_markdup_command = (
"sambamba markdup -t %d %s %s %s"
- % (cpu_count(), sambamba_parms, bam, tmp_dup_mark_filename)
+ % (cpu_count(), sambamba_params, bam, tmp_dup_mark_filename)
)
logger.info(sambamba_markdup_command)
subprocess.check_call(
--
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