Fix missing libraries and use of python3.

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
     """
   }
 

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')