From 13fe4335df882a5c39529f0a3e2b12a71bb97516 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Tue, 3 Oct 2017 16:27:54 -0500
Subject: [PATCH] Update trim_reads to extrapolate the params.
---
workflow/scripts/trim_reads.py | 11 ++++++-----
1 file changed, 6 insertions(+), 5 deletions(-)
diff --git a/workflow/scripts/trim_reads.py b/workflow/scripts/trim_reads.py
index 4ab3ffe..4a2d728 100644
--- a/workflow/scripts/trim_reads.py
+++ b/workflow/scripts/trim_reads.py
@@ -8,7 +8,6 @@ import argparse
import shutil
import logging
import sys
-import json
EPILOG = '''
For more details:
@@ -67,11 +66,13 @@ def trim_reads(fastq, paired):
'''Run trim_galore on 1 or 2 files.'''
if paired: # paired-end data
- trim_command = "trim_galore --paired -q 25 --illumina --gzip --length 35 " \
- + " ".join(fastq)
+ trim_params = '--paired -q 25 --illumina --gzip --length 35'
+ trim_command = "trim_galore %s %s %s " \
+ % (trim_params, fastq[0], fastq[1])
else:
- trim_command = "trim_galore -q 25 --illumina --gzip --length 35 " \
- + " ".join(fastq)
+ trim_params = '-q 25 --illumina --gzip --length 35'
+ trim_command = "trim_galore %s %s " \
+ % (trim_params, fastq[0])
logger.info("Running trim_galore with %s", trim_command)
--
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