From 5532fa6d2d0fb0f8bd120ab0edc899bb6fd15aff Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Tue, 3 Oct 2017 14:13:17 -0500
Subject: [PATCH] Add in argument for trim_parameters.
---
workflow/scripts/trim_reads.py | 18 ++++++++++++++----
1 file changed, 14 insertions(+), 4 deletions(-)
diff --git a/workflow/scripts/trim_reads.py b/workflow/scripts/trim_reads.py
index 29d9b92..c0f80a2 100644
--- a/workflow/scripts/trim_reads.py
+++ b/workflow/scripts/trim_reads.py
@@ -34,6 +34,11 @@ def get_args():
nargs='+',
required=True)
+ parser.add_argument('-p', '--paired',
+ help="True/False if paired-end or single end.",
+ default=False,
+ action='store_true')
+
args = parser.parse_args()
return args
@@ -58,10 +63,15 @@ def check_tools():
raise Exception('Missing cutadapt')
-def trim_reads(fastq):
+def trim_reads(fastq, paired):
'''Run trim_galore on 1 or 2 files.'''
- qc_command = "trim_galore --paired -q 25 --illumina --gzip --length 35 " \
- + " ".join(fastq)
+
+ if paired: # paired-end data
+ qc_command = "trim_galore --paired -q 25 --illumina --gzip --length 35 " \
+ + " ".join(fastq)
+ else:
+ qc_command = "trim_galore -q 25 --illumina --gzip --length 35 " \
+ + " ".join(fastq)
logger.info("Running trim_galore with %s", qc_command)
@@ -80,7 +90,7 @@ def main():
check_tools()
# Run trim_reads
- trim_reads(args.fastq)
+ trim_reads(args.fastq, args.paired)
if __name__ == '__main__':
--
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