let bwa_mem
?(configuration = Tools.Bwa.Configuration.Mem.default) =
make_aligner "bwamem" ~configuration
~config_name:Tools.Bwa.Configuration.Mem.name
~config_to_json:Tools.Bwa.Configuration.Mem.to_json
~make_workflow:(
fun
~reference_build
~configuration ~result_prefix ~run_with freads ->
Tools.Bwa.mem_align_to_sam
~reference_build ~configuration ~fastq:freads
~result_prefix ~run_with ()
|> Tools.Samtools.sam_to_bam ~reference_build ~run_with
)