#if $reference_source.reference_source_selector == 'history':
        ln -f -s '$reference_source.ref_file' reference.fa &&
    #else:
        ln -f -s '$reference_source.ref_file.fields.path' reference.fa &&
    #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 &&    

nextalign run
    --input-ref reference.fa
    --output-fasta '$output_fasta'
#if $output_insertions:
    --output-insertions '$output_csv'
#end if
#if $translation.translation_select == "yes":
    --genes '${translation.genes}'
    --genemap '${translation.genemap}'
    --output-translations 'sequences.gene.{gene}.fasta'
#end if
    --min-length ${min_length}
    --penalty-gap-extend ${penalty_gap_extend}
    --penalty-gap-open ${penalty_gap_open}
    --penalty-gap-open-in-frame ${penalty_gap_open_in_frame}
    --penalty-gap-open-out-of-frame ${penalty_gap_open_out_of_frame}
    --penalty-mismatch ${penalty_mismatch}
    --score-match ${score_match}
    --max-indel ${max_indel}
    --seed-length ${seed_length}
    --min-seeds ${min_seeds}
    --seed-spacing ${seed_spacing}
    --mismatches-allowed ${mismatches_allowed}
    $query