let hisat
?(configuration = Tools.Hisat.Configuration.default_v1) =
make_aligner "hisat"
~configuration
~config_name:Tools.Hisat.Configuration.name
~config_to_json:Tools.Hisat.Configuration.to_json
~make_workflow:(
fun ~reference_build ~configuration ~result_prefix ~run_with fastq ->
Tools.Hisat.align ~configuration ~reference_build
~fastq ~result_prefix ~run_with ()
|> Tools.Samtools.sam_to_bam ~reference_build ~run_with
)