From 970fea4b71d9d8eed47f93080233bd8fb13ec9e3 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Fri, 6 Oct 2017 13:59:22 -0500
Subject: [PATCH] Use python3 for testing the design file and use local for
this.
---
workflow/conf/biohpc.config | 1 +
workflow/main.nf | 2 +-
2 files changed, 2 insertions(+), 1 deletion(-)
diff --git a/workflow/conf/biohpc.config b/workflow/conf/biohpc.config
index f05eca9..8e78791 100644
--- a/workflow/conf/biohpc.config
+++ b/workflow/conf/biohpc.config
@@ -5,6 +5,7 @@ process {
// Process specific configuration
$checkDesignFile {
module = ['python/3.6.1-2-anaconda']
+ executor = 'local'
}
$trim_galore {
module = ['python/3.6.1-2-anaconda', 'trimgalore/0.4.1']
diff --git a/workflow/main.nf b/workflow/main.nf
index b6d1bfb..9b9980e 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -48,7 +48,7 @@ process checkDesignFile {
if (pairedEnd) {
"""
- python $baseDir/scripts/check_design.py -d $designFile -f $readsList -p
+ python3 $baseDir/scripts/check_design.py -d $designFile -f $readsList -p
"""
}
else {
--
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