--- a/seqsero2S.xml	Mon Sep 29 20:04:28 2025 +0000
+++ b/seqsero2S.xml	Wed Jan 21 19:30:21 2026 +0000
@@ -36,14 +36,14 @@
         ln -s $forward ${name}_1.fastq;
         ln -s $reverse ${name}_2.fastq;
       #else 
-        #set $name = $reads.assembly.name.replace(' ', '_')
-        #set $ga = $reads.assembly
-        #set $infile = $name + ".fasta" 
-        ln -s $ga ${name}.fasta;
+        #set $name = "$reads.assembly.name.replace(' ', '_')"
+        #set $ga = "$reads.assembly"
+        #set $infile = $name + .fasta 
+        ln -s $ga "$infile";
         #set $tval = 4
         #set $mode='k'
       #end if
-      echo $name ;
+      echo "$name" ;
       echo "-=-=-=-=-" ;
       touch output/SeqSero_log.txt ;
       /usr/local/bin/SeqSero2S.py --version ;
@@ -56,7 +56,7 @@
       #if $mode == 'a':
         -b $maptype 
       #end if
-        -i $infile &&
+        -i "$infile" &&
         echo "-=-=-=-=-" &&
         cat output/SeqSero_log.txt &&
         echo "-=-=-=-=-" &&