sig
  type input_fastq =
      [ `Paired_end of
          Biokepi_pipeline_edsl.Pipeline.File.t list *
          Biokepi_pipeline_edsl.Pipeline.File.t list
      | `Single_end of Biokepi_pipeline_edsl.Pipeline.File.t list ]
  val input_fastq :
    dataset:string ->
    Biokepi_pipeline_edsl.Pipeline.Construct.input_fastq ->
    Biokepi_pipeline_edsl.Pipeline.fastq_sample
    Biokepi_pipeline_edsl.Pipeline.t
  val bam :
    dataset:string ->
    Biokepi_pipeline_edsl.Pipeline.bam ->
    Biokepi_pipeline_edsl.Pipeline.bam Biokepi_pipeline_edsl.Pipeline.t
  val bam_to_fastq :
    ?sample_name:Biokepi_pipeline_edsl.Pipeline.fastq_sample_info ->
    [ `Paired | `Single ] ->
    Biokepi_pipeline_edsl.Pipeline.bam Biokepi_pipeline_edsl.Pipeline.t ->
    Biokepi_pipeline_edsl.Pipeline.fastq_sample
    Biokepi_pipeline_edsl.Pipeline.t
  val bwa :
    ?configuration:Biokepi_bfx_tools.Bwa.Configuration.Aln.t ->
    Biokepi_pipeline_edsl.Pipeline.fastq_sample
    Biokepi_pipeline_edsl.Pipeline.t ->
    Biokepi_pipeline_edsl.Pipeline.bam Biokepi_pipeline_edsl.Pipeline.t
  val bwa_aln :
    ?configuration:Biokepi_bfx_tools.Bwa.Configuration.Aln.t ->
    Biokepi_pipeline_edsl.Pipeline.fastq_sample
    Biokepi_pipeline_edsl.Pipeline.t ->
    Biokepi_pipeline_edsl.Pipeline.bam Biokepi_pipeline_edsl.Pipeline.t
  val bwa_mem :
    ?configuration:Biokepi_bfx_tools.Bwa.Configuration.Mem.t ->
    Biokepi_pipeline_edsl.Pipeline.fastq_sample
    Biokepi_pipeline_edsl.Pipeline.t ->
    Biokepi_pipeline_edsl.Pipeline.bam Biokepi_pipeline_edsl.Pipeline.t
  val mosaik :
    Biokepi_pipeline_edsl.Pipeline.fastq_sample
    Biokepi_pipeline_edsl.Pipeline.t ->
    Biokepi_pipeline_edsl.Pipeline.bam Biokepi_pipeline_edsl.Pipeline.t
  val star :
    ?configuration:Biokepi_bfx_tools.Star.Configuration.Align.t ->
    Biokepi_pipeline_edsl.Pipeline.fastq_sample
    Biokepi_pipeline_edsl.Pipeline.t ->
    Biokepi_pipeline_edsl.Pipeline.bam Biokepi_pipeline_edsl.Pipeline.t
  val hisat :
    ?configuration:Biokepi_bfx_tools.Hisat.Configuration.t ->
    Biokepi_pipeline_edsl.Pipeline.fastq_sample
    Biokepi_pipeline_edsl.Pipeline.t ->
    Biokepi_pipeline_edsl.Pipeline.bam Biokepi_pipeline_edsl.Pipeline.t
  val stringtie :
    ?configuration:Biokepi_bfx_tools.Stringtie.Configuration.t ->
    Biokepi_pipeline_edsl.Pipeline.bam Biokepi_pipeline_edsl.Pipeline.t ->
    Biokepi_pipeline_edsl.Pipeline.gtf Biokepi_pipeline_edsl.Pipeline.t
  val gatk_indel_realigner :
    ?configuration:Biokepi_bfx_tools.Gatk.Configuration.indel_realigner ->
    Biokepi_pipeline_edsl.Pipeline.bam Biokepi_pipeline_edsl.Pipeline.t ->
    Biokepi_pipeline_edsl.Pipeline.bam Biokepi_pipeline_edsl.Pipeline.t
  val picard_mark_duplicates :
    ?settings:Biokepi_bfx_tools.Picard.Mark_duplicates_settings.t ->
    Biokepi_pipeline_edsl.Pipeline.bam Biokepi_pipeline_edsl.Pipeline.t ->
    Biokepi_pipeline_edsl.Pipeline.bam Biokepi_pipeline_edsl.Pipeline.t
  val gatk_bqsr :
    ?configuration:Biokepi_bfx_tools.Gatk.Configuration.bqsr ->
    Biokepi_pipeline_edsl.Pipeline.bam Biokepi_pipeline_edsl.Pipeline.t ->
    Biokepi_pipeline_edsl.Pipeline.bam Biokepi_pipeline_edsl.Pipeline.t
  val pair :
    normal:Biokepi_pipeline_edsl.Pipeline.bam
           Biokepi_pipeline_edsl.Pipeline.t ->
    tumor:Biokepi_pipeline_edsl.Pipeline.bam Biokepi_pipeline_edsl.Pipeline.t ->
    Biokepi_pipeline_edsl.Pipeline.bam_pair Biokepi_pipeline_edsl.Pipeline.t
  val germline_variant_caller :
    Biokepi_pipeline_edsl.Pipeline.germline
    Biokepi_pipeline_edsl.Pipeline.Variant_caller.t ->
    Biokepi_pipeline_edsl.Pipeline.bam Biokepi_pipeline_edsl.Pipeline.t ->
    Biokepi_pipeline_edsl.Pipeline.vcf Biokepi_pipeline_edsl.Pipeline.t
  val gatk_haplotype_caller :
    Biokepi_pipeline_edsl.Pipeline.bam Biokepi_pipeline_edsl.Pipeline.t ->
    Biokepi_pipeline_edsl.Pipeline.vcf Biokepi_pipeline_edsl.Pipeline.t
  val somatic_variant_caller :
    Biokepi_pipeline_edsl.Pipeline.somatic
    Biokepi_pipeline_edsl.Pipeline.Variant_caller.t ->
    Biokepi_pipeline_edsl.Pipeline.bam_pair Biokepi_pipeline_edsl.Pipeline.t ->
    Biokepi_pipeline_edsl.Pipeline.vcf Biokepi_pipeline_edsl.Pipeline.t
  val mutect :
    ?configuration:Biokepi_bfx_tools.Mutect.Configuration.t ->
    Biokepi_pipeline_edsl.Pipeline.bam_pair Biokepi_pipeline_edsl.Pipeline.t ->
    Biokepi_pipeline_edsl.Pipeline.vcf Biokepi_pipeline_edsl.Pipeline.t
  val mutect2 :
    ?configuration:Biokepi_bfx_tools.Gatk.Configuration.Mutect2.t ->
    Biokepi_pipeline_edsl.Pipeline.bam_pair Biokepi_pipeline_edsl.Pipeline.t ->
    Biokepi_pipeline_edsl.Pipeline.vcf Biokepi_pipeline_edsl.Pipeline.t
  val somaticsniper :
    ?configuration:Biokepi_bfx_tools.Somaticsniper.Configuration.t ->
    Biokepi_pipeline_edsl.Pipeline.bam_pair Biokepi_pipeline_edsl.Pipeline.t ->
    Biokepi_pipeline_edsl.Pipeline.vcf Biokepi_pipeline_edsl.Pipeline.t
  val varscan_somatic :
    ?adjust_mapq:int ->
    Biokepi_pipeline_edsl.Pipeline.bam_pair Biokepi_pipeline_edsl.Pipeline.t ->
    Biokepi_pipeline_edsl.Pipeline.vcf Biokepi_pipeline_edsl.Pipeline.t
  val strelka :
    configuration:Biokepi_bfx_tools.Strelka.Configuration.t ->
    Biokepi_pipeline_edsl.Pipeline.bam_pair Biokepi_pipeline_edsl.Pipeline.t ->
    Biokepi_pipeline_edsl.Pipeline.vcf Biokepi_pipeline_edsl.Pipeline.t
  val virmid :
    configuration:Biokepi_bfx_tools.Virmid.Configuration.t ->
    Biokepi_pipeline_edsl.Pipeline.bam_pair Biokepi_pipeline_edsl.Pipeline.t ->
    Biokepi_pipeline_edsl.Pipeline.vcf Biokepi_pipeline_edsl.Pipeline.t
  val muse :
    configuration:Biokepi_bfx_tools.Muse.Configuration.t ->
    Biokepi_pipeline_edsl.Pipeline.bam_pair Biokepi_pipeline_edsl.Pipeline.t ->
    Biokepi_pipeline_edsl.Pipeline.vcf Biokepi_pipeline_edsl.Pipeline.t
  val seq2hla :
    Biokepi_pipeline_edsl.Pipeline.fastq_sample
    Biokepi_pipeline_edsl.Pipeline.t ->
    Biokepi_pipeline_edsl.Pipeline.seq2hla_hla_types
    Biokepi_pipeline_edsl.Pipeline.t
  val optitype :
    [ `DNA | `RNA ] ->
    Biokepi_pipeline_edsl.Pipeline.fastq_sample
    Biokepi_pipeline_edsl.Pipeline.t ->
    Biokepi_pipeline_edsl.Pipeline.optitype_hla_types
    Biokepi_pipeline_edsl.Pipeline.t
  val add_tags :
    ?recursively:bool ->
    string list ->
    'a Biokepi_pipeline_edsl.Pipeline.t ->
    'a Biokepi_pipeline_edsl.Pipeline.t
end