From adf18e0625ee6587a3fe35f85eb5fc55c7f2a9c5 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Mon, 9 Oct 2017 17:24:13 -0500
Subject: [PATCH] Update incorrect line break.
---
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 20f02ae..d4fbaaa 100644
--- a/workflow/scripts/map_qc.py
+++ b/workflow/scripts/map_qc.py
@@ -194,7 +194,7 @@ def dedup_mapped(bam, bam_basename, paired):
# Generate mapping statistics
final_bam_file_mapstats_filename = final_bam_prefix + ".flagstat.qc"
with open(final_bam_file_mapstats_filename, 'w') as fh:
- flagstat_command = "sambamba flagstat -t %d %s"
+ flagstat_command = "sambamba flagstat -t %d %s" \
% (cpu_count(), final_bam_filename)
logger.info(flagstat_command)
subprocess.check_call(shlex.split(flagstat_command), stdout=fh)
--
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