## initialize

        #if $reference_source.reference_source_selector == 'history':
            #if $reference_source.ref_file.ext.endswith(".gz")
                gunzip -c '$reference_source.ref_file' > reference.fa &&
            #else
                cp '$reference_source.ref_file' reference.fa &&
            #end if
        #else:
            cp '$reference_source.ref_file.fields.path' reference.fa &&
        #end if
    


#if $pool.pool_mode == "Yes":
    ## run
    medaka vcf
    ## optional
    --debug
    #if $regions
        --regions '${regions}'
    #end if
    $verbose
    ${ambig_ref}
    ${gvcf}
    ## required
    #for $current in $pool.inputs
        '$current'
    #end for
    reference.fa
#elif $pool.pool_mode == "No":
    ## run
    medaka vcf
    ## optional
    --debug
    #if $regions
        --regions '${regions}'
    #end if
    $verbose
    ${ambig_ref}
    ${gvcf}
    ## required
    '$pool.input'
    reference.fa
#end if
#if str($output_annotated.output_annotated_select) == 'false':
    '$out_variants' 2>&1 | tee log.txt
#else
    raw.vcf 2>&1 | tee log.txt
    && ln -s '$output_annotated.in_bam' in.bam
    && ln -s '$output_annotated.in_bam.metadata.bam_index' in.bai
    && medaka tools annotate --dpsp --pad $output_annotated.pad raw.vcf reference.fa in.bam tmp.vcf
    && python '$__tool_directory__/convert_VCF_info_fields.py' tmp.vcf '$out_variants'
#end if