From 08898dde8e3df55326b01b980b933ab4977f897d Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Fri, 6 Oct 2017 11:21:38 -0500
Subject: [PATCH] Fix file used in first step.
---
workflow/scripts/map_reads.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/workflow/scripts/map_reads.py b/workflow/scripts/map_reads.py
index 4fd4d21..552a2d9 100644
--- a/workflow/scripts/map_reads.py
+++ b/workflow/scripts/map_reads.py
@@ -100,7 +100,7 @@ def generate_sa(fastq, reference):
with open(sai, 'w') as sai_file:
bwa_command = "bwa aln %s -t %d %s %s" \
% (bwa_aln_params, cpu_count(),
- reference, fastq_basename)
+ reference, fastq)
logger.info("Running bwa with %s", bwa_command)
subprocess.check_call(shlex.split(bwa_command), stdout=sai_file)
--
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