## Set up samples list file.
        #if $sample_names.strip() != '':
           echo $sample_names | awk -F ',' '{ for (i = 1; i <= NF; i++) { print \$i; } }' > samples_list.txt &&
        #end if

        ## Set up command + input.
        varscan ${cmd} '${input}'
            --min-coverage ${min_coverage} 
            --min-reads2 ${min_reads2} 
            --min-avg-qual ${min_avg_qual}
            --min-var-freq ${min_var_freq}
            --min-freq-for-hom ${min_freq_for_hom}
            --p-value ${p_value}

            #if str($strand_filter) == 'yes':
              --strand-filter 1
            #end if

            ## Report only variants in consensus.
            #if str($cmd) == 'mpileup2cns':
              --variants
            #end if
            
            ## Set up outputs.
            --output-vcf 1 > '$output'

            #if $sample_names.strip() != '':
                --vcf-sample-list samples_list.txt
            #end if