replacing special character with _ to match with files in files/

Author: mshakya

src/runPhaME.pl

@@ -315,6 +315,7 @@
    print "Complete\n";
 } # check=0
 
+$name =~ s/\W/_/g; # Replacing special characters with _
 $reference = "$workdir/files/$name.fna";
 
 if ($nucmer==1){