mkdir gemini &&
        ln -s '${annotation_databases.fields.path}/gemini/data' gemini/data &&
        export GEMINI_CONFIG='${annotation_databases.fields.path}' &&
    

        ## gemini load expects a bgzipped and tabixed vcf as input
        #set $tabixed_file = 'input.vcf.gz'
        #if $infile.ext == 'vcf':
            bgzip -c '$infile' > $tabixed_file &&
            tabix -p vcf $tabixed_file &&
        #else:
            ln -s '$infile' $tabixed_file &&
            ln -s '$infile.metadata.tabix_index' ${tabixed_file}.tbi &&
        #end if

        gemini
            load
            -v input.vcf.gz
            #if str( $annotation_type ) != "None":
                -t $annotation_type
            #end if

            $has_genotypes

            #if $ped:
                -p $ped
            #end if

            #if 'gerp_bp' not in str($opt_content):
                --skip-gerp-bp
            #end if
            #if 'cadd' not in str($opt_content):
                --skip-cadd
            #end if
            #if 'gene_tables' not in str($opt_content):
                --skip-gene-tables
            #end if
            #if 'genotypes' not in str($opt_content):
                --no-load-genotypes
            #end if
            #if 'gt_pl' not in str($opt_content):
                --skip-pls
            #end if
            #if 'passonly' in str($opt_content):
                --passonly
            #end if
            #if 'info_string' in str($opt_content):
                --save-info-string
            #end if

            --cores \${GALAXY_SLOTS:-4}

            '$outfile'