From fd33ecb774d26d7ecc18d413f34129528ce2e633 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Tue, 3 Oct 2017 15:42:11 -0500
Subject: [PATCH] Update trim command name.
---
workflow/scripts/trim_reads.py | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/workflow/scripts/trim_reads.py b/workflow/scripts/trim_reads.py
index c0f80a2..4ab3ffe 100644
--- a/workflow/scripts/trim_reads.py
+++ b/workflow/scripts/trim_reads.py
@@ -67,16 +67,16 @@ def trim_reads(fastq, paired):
'''Run trim_galore on 1 or 2 files.'''
if paired: # paired-end data
- qc_command = "trim_galore --paired -q 25 --illumina --gzip --length 35 " \
+ trim_command = "trim_galore --paired -q 25 --illumina --gzip --length 35 " \
+ " ".join(fastq)
else:
- qc_command = "trim_galore -q 25 --illumina --gzip --length 35 " \
+ trim_command = "trim_galore -q 25 --illumina --gzip --length 35 " \
+ " ".join(fastq)
- logger.info("Running trim_galore with %s", qc_command)
+ logger.info("Running trim_galore with %s", trim_command)
- qual_fastq = subprocess.Popen(qc_command, shell=True)
- out, err = qual_fastq.communicate()
+ trim = subprocess.Popen(trim_command, shell=True)
+ out, err = trim.communicate()
def main():
--
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