--- a/bbduk.xml	Fri Apr 12 20:20:01 2024 +0000
+++ b/bbduk.xml	Wed Apr 24 20:24:48 2024 +0000
@@ -7,7 +7,6 @@
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
 #import os
-#import re
 
 #if str($input_type_cond.input_type) in ['single', 'pair']:
     #set read1 = $input_type_cond.read1
@@ -25,17 +24,15 @@
     #end if
 #else:
     #set read1 = $input_type_cond.reads_collection['forward']
-    #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.name))
     ## bbduk uses the file extension to determine the input format.
-    #set ext = $read1_identifier + '.fastq'
+    #set ext = '.fastq'
     #if $read1.ext.endswith('.gz'):
         #set ext = $ext + '.gz'
     #end if
-    #set read1_file = $read1_identifier + $ext
+    #set read1_file = 'forward' + $ext
     ln -s '${read1}' '${read1_file}' &&
     #set read2 = $input_type_cond.reads_collection['reverse']
-    #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.name))
-    #set read2_file = $read2_identifier + $ext
+    #set read2_file = 'reverse' + $ext
     ln -s '${read2}' '${read2_file}' &&
 #end if