From 861b7993345e02ca9a816d5e795a7207488b1cf7 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Fri, 6 Oct 2017 09:54:55 -0500
Subject: [PATCH] Fix missing libraries and use of python3.
---
workflow/main.nf | 4 ++--
workflow/scripts/map_reads.py | 3 ++-
2 files changed, 4 insertions(+), 3 deletions(-)
diff --git a/workflow/main.nf b/workflow/main.nf
index 4494a86..b6d1bfb 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -119,12 +119,12 @@ process alignReads {
if (pairedEnd) {
"""
- python $baseDir/scripts/map_reads.py -f ${reads[0]} ${reads[1]} -r ${index}/genome.fa -p
+ python3 $baseDir/scripts/map_reads.py -f $reads -r ${index}/genome.fa -p
"""
}
else {
"""
- python $baseDir/scripts/map_reads.py -f ${reads[0]} -r ${index}/genome.fa
+ python3 $baseDir/scripts/map_reads.py -f $reads -r ${index}/genome.fa
"""
}
diff --git a/workflow/scripts/map_reads.py b/workflow/scripts/map_reads.py
index e3a8d46..4fd4d21 100644
--- a/workflow/scripts/map_reads.py
+++ b/workflow/scripts/map_reads.py
@@ -6,6 +6,7 @@ import os
import subprocess
import argparse
import shutil
+import shlex
import logging
import sys
from multiprocessing import cpu_count
@@ -74,7 +75,7 @@ def check_tools():
logger.info('Checking for required libraries and components on this system')
bwa_path = shutil.which("bwa")
- if trimgalore_path:
+ if bwa_path:
logger.info('Found bwa: %s', bwa_path)
else:
logger.error('Missing bwa')
--
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