#import re

        mkdir stacks_outputs

        &&

        #for $input_file in $input_col
            #set $filename = str($input_file.element_identifier)
            #if not $filename.endswith('.tsv')
                #set $filename = $filename + ".tsv"
            #end if
            #if re.search('\.(tags|snps|alleles|matches)(\.tsv)?$', $filename)
                ln -s '${input_file}' 'stacks_outputs/${filename}' &&
            #end if
        #end for

        genotypes

            -P stacks_outputs
            -b $advanced_options.batchid

            -t $options_usage.cross_type
            -o $options_usage.map_out.map_out_type

            #if str( $options_usage.map_out.map_out_type ) == "genomic"
                -e ${options_usage.map_out.enzyme}
            #end if

            #if str($advanced_options.minprogeny)
                -r $advanced_options.minprogeny
            #end if

            #if str($advanced_options.mindepth)
                -m $advanced_options.mindepth
            #end if

            #if str($advanced_options.lnl)
                --lnl_lim $advanced_options.lnl
            #end if

            #if $advanced_options.blacklist
                -B '$advanced_options.blacklist'
            #end if
            #if $advanced_options.whitelist
                -W '$advanced_options.whitelist'
            #end if

            #if $advanced_options.manual_cor
                --corr_path '$advanced_options.manual_cor'
            #end if

            #if $options_autocorr.corrections != ""
                -c
                --min_hom_seqs $options_autocorr.hom
                --min_het_seqs $options_autocorr.het
                --max_het_seqs $options_autocorr.hetmax
            #end if

            ## output SQL file (as denovo/refmap)
            -s

            
        
        ## We need to do this as the output file names contains the value of an option (min progeny)
        &&
        cd stacks_outputs/ &&
        ln -s batch_1.genotypes_*onemap.tsv batch_1.genotypes.onemap.tsv &&
        ln -s batch_1.genotypes_*.onemap.txt batch_1.genotypes.onemap.txt &&
        ln -s batch_1.genomic_*.tsv batch_1.genomic.tsv &&
        ln -s batch_1.genotypes_*.rqtl.tsv batch_1.genotypes.rqtl.tsv &&
        ln -s batch_1.haplotypes_*.tsv batch_1.haplotypes.tsv &&
        ln -s batch_1.genotypes_*.loc batch_1.genotypes.loc &&
        ln -s batch_1.genotypes_*.txt batch_1.genotypes.txt &&
        ln -s batch_1.genotypes_*[^rqtl].tsv batch_1.genotypes.tsv &&
        cd ..
        
    

            &&

            stacks_summary.py --stacks-prog genotypes --res-dir stacks_outputs --summary stacks_outputs/summary.html