From 31ffef2741626363c8e77448df5db514d7d5c354 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Tue, 3 Oct 2017 14:07:13 -0500
Subject: [PATCH] update path variables
---
workflow/scripts/trim_reads.py | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/workflow/scripts/trim_reads.py b/workflow/scripts/trim_reads.py
index dae4605..faac921 100644
--- a/workflow/scripts/trim_reads.py
+++ b/workflow/scripts/trim_reads.py
@@ -44,14 +44,14 @@ def check_tools():
logger.info('Checking for required libraries and components on this system')
trimgalore_path = shutil.which("trim_galore")
- if fastqc_path:
+ if trimgalore_path:
logger.info('Found trimgalore: %s', fastqc_path)
else:
logger.error('Missing trimgalore')
raise Exception('Missing trimgalore')
cutadapt_path = shutil.which("cutadapt")
- if fastqc_path:
+ if cutadapt_path:
logger.info('Found cutadapt: %s', fastqc_path)
else:
logger.error('Missing cutadapt')
--
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