let from_fastqs_with_variant_caller
~variant_caller ~normal_fastqs ~tumor_fastqs ~dataset =
let open Pipeline.Construct in
let normal = input_fastq ~dataset normal_fastqs in
let tumor = input_fastq ~dataset tumor_fastqs in
let make_bam data =
data |> bwa_mem |> gatk_indel_realigner |> picard_mark_duplicates |> gatk_bqsr
in
let vc_input =
pair ~normal:(make_bam normal) ~tumor:(make_bam tumor) in
[variant_caller vc_input]