#if $db.source == "cached"
            ln -s '${db.release.fields.path}' db &&
        #elif $db.source == "download"
            nextclade dataset get -n '${organism}' -o db &&
        #end if 
        
    #if $input_fasta.is_of_type('fasta.gz')
        #set $query = 'query.fa.gz'
    #else
        #set $query = 'query.fa'
    #end if
    ln -s '$input_fasta' $query &&    

        nextclade run
        --input-dataset db/
        #if $adv.advanced_options == 'yes'
            #if $adv.input_qc_config
                --input-qc-config '$adv.input_qc_config'
            #end if
            #if $adv.input_root_seq
                --input-root-seq '$adv.input_root_seq'
            #end if
            #if $adv.input_tree
                --input-tree '$adv.input_tree'
            #end if
            #if $adv.input_gene_map
                --input-gene-map '$adv.input_gene_map'
            #end if 
            #if $adv.input_pcr_primers
                --input-pcr-primers '$adv.input_pcr_primers'
            #end if
            #if $adv.input_virus_properties
                --input-virus-properties '$adv.input_virus_properties'
            #end if
        #end if
        #if $outputs and "report_tsv" in $outputs
            #if $include_header
                --output-tsv '$report_tsv'
            #else
                --output-tsv report.tsv
            #end if
        #end if 
        #if $outputs and "report_json" in $outputs
            --output-json '${report_json}'
        #end if 
        #if $outputs and "output_tree" in $outputs
            --output-tree '${output_tree}'
        #end if
        #if $outputs and "output_fasta" in $outputs
            --output-fasta "${output_fasta}"
            #if str($adv.advanced_options) == "yes"
                $adv.include_reference
            #end if
        #end if
        $query
        #if $outputs and "report_tsv" in $outputs and not $include_header
            && tail -n+2 report.tsv >'$report_tsv'
        #end if