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Commit 08898dde authored by Venkat Malladi's avatar Venkat Malladi
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Fix file used in first step.

parent 861b7993
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......@@ -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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