mkdir stacks_inputs reads stacks_outputs
        &&
        #for $input_file in $stacks_col
            #set $ext = ""
            #if not str($input_file.element_identifier).endswith('.tsv')
                #set $ext = ".tsv"
            #end if
            ln -s '${input_file}' 'stacks_inputs/${input_file.element_identifier}${ext}' &&
        #end for

        #for $input_file in $reads
            #set $name = str($input_file.element_identifier)
            ## sort_read_pairs is expecting strange fastq names: <sample_name>.fq_2
            #if $name.endswith('.1.fq')
                ## handle a common case
                #set $name = $name[:-5]+".fq_1"
            #else if $name.endswith('.2.fq')
                ## handle a common case
                #set $name = $name[:-5]+".fq_2"
            #else if not $name.endswith('.fq') and not $name.endswith('.fq_2')
                ## no extension, consider it's a fq_2 file
                #set $name = $name + ".fq_2"
            #end if
            ln -s '${input_file}' 'reads/${name}' &&
        #end for

        sort_read_pairs.pl
            -p stacks_inputs
            -s 'reads'

            #if $whitelist
                -w '$whitelist'
            #end if

            #if $threshold
                -r $threshold
            #end if

            -o stacks_outputs

        #if $velvet.use_velvet == "yes"
            ## remove possible empty files
            && find stacks_outputs -type f -size 0 -exec rm {} \;

            &&
            mkdir assembled
            &&
            velvet_path=`which velveth` && velvet_path=`dirname "\$velvet_path"`
            &&
            exec_velvet.pl -s stacks_outputs -o assembled -c -M ${velvet.contig_length} -e "\$velvet_path"
        #end if