diff --git a/workflow/main.nf b/workflow/main.nf index 4494a861280aee1b56c4775de4bb29a59fd7a63d..b6d1bfb4e1cea1ed67dffc951c70584233370cd9 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 e3a8d466f7fbd04fb4dd4d47cde7cae220dc380a..4fd4d211460d54bbd13ffb72e7daec83092d71da 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')