Module type Biokepi.EDSL.Semantics

module type Semantics = Biokepi_pipeline_edsl.Semantics.Bioinformatics_base

include Biokepi_pipeline_edsl.Semantics.Lambda_with_list_operations

val pair : 'a repr -> 'b repr -> ('a * 'b) repr

val pair_first : ('a * 'b) repr -> 'a repr

val pair_second : ('a * 'b) repr -> 'b repr

val to_unit : 'a repr -> unit repr

val fastq : sample_name:string ->
       ?fragment_id:string -> r1:string -> ?r2:string -> unit -> [ `Fastq ] repr

val fastq_gz : sample_name:string ->
       ?fragment_id:string ->
       r1:string -> ?r2:string -> unit -> [ `Gz of [ `Fastq ] ] repr

val bam : path:string ->
       ?sorting:[ `Coordinate | `Read_name ] ->
       reference_build:string -> unit -> [ `Bam ] repr

val gunzip : [ `Gz of 'a ] repr -> 'a repr

val gunzip_concat : [ `Gz of 'a ] list repr -> 'a repr

val concat : 'a list repr -> 'a repr

val merge_bams : [ `Bam ] list repr -> [ `Bam ] repr

val bam_to_fastq : sample_name:string ->
       ?fragment_id:string -> [ `PE | `SE ] -> [ `Bam ] repr -> [ `Fastq ] repr

val bwa_aln : ?configuration:Biokepi_bfx_tools.Bwa.Configuration.Aln.t ->
       reference_build:Biokepi_run_environment.Reference_genome.name ->
       [ `Fastq ] repr -> [ `Bam ] repr

val bwa_mem : ?configuration:Biokepi_bfx_tools.Bwa.Configuration.Mem.t ->
       reference_build:Biokepi_run_environment.Reference_genome.name ->
       [ `Fastq ] repr -> [ `Bam ] repr

val star : ?configuration:Biokepi_bfx_tools.Star.Configuration.Align.t ->
       reference_build:Biokepi_run_environment.Reference_genome.name ->
       [ `Fastq ] repr -> [ `Bam ] repr

val hisat : ?configuration:Biokepi_bfx_tools.Hisat.Configuration.t ->
       reference_build:Biokepi_run_environment.Reference_genome.name ->
       [ `Fastq ] repr -> [ `Bam ] repr

val mosaik : reference_build:Biokepi_run_environment.Reference_genome.name ->
       [ `Fastq ] repr -> [ `Bam ] repr

val stringtie : ?configuration:Biokepi_bfx_tools.Stringtie.Configuration.t ->
       [ `Bam ] repr -> [ `Gtf ] repr

val gatk_indel_realigner : ?configuration:Biokepi_bfx_tools.Gatk.Configuration.indel_realigner ->
       [ `Bam ] repr -> [ `Bam ] repr

val gatk_indel_realigner_joint : ?configuration:Biokepi_bfx_tools.Gatk.Configuration.indel_realigner ->
       ([ `Bam ] * [ `Bam ]) repr -> ([ `Bam ] * [ `Bam ]) repr

val picard_mark_duplicates : ?configuration:Biokepi_bfx_tools.Picard.Mark_duplicates_settings.t ->
       [ `Bam ] repr -> [ `Bam ] repr

val gatk_bqsr : ?configuration:Biokepi_bfx_tools.Gatk.Configuration.bqsr ->
       [ `Bam ] repr -> [ `Bam ] repr

val seq2hla : [ `Fastq ] repr -> [ `Seq2hla_result ] repr

val optitype : [ `DNA | `RNA ] -> [ `Fastq ] repr -> [ `Optitype_result ] repr

val gatk_haplotype_caller : [ `Bam ] repr -> [ `Vcf ] repr

val mutect : ?configuration:Biokepi_bfx_tools.Mutect.Configuration.t ->
       normal:[ `Bam ] repr -> tumor:[ `Bam ] repr -> unit -> [ `Vcf ] repr

val mutect2 : ?configuration:Biokepi_bfx_tools.Gatk.Configuration.Mutect2.t ->
       normal:[ `Bam ] repr -> tumor:[ `Bam ] repr -> unit -> [ `Vcf ] repr

val somaticsniper : ?configuration:Biokepi_bfx_tools.Somaticsniper.Configuration.t ->
       normal:[ `Bam ] repr -> tumor:[ `Bam ] repr -> unit -> [ `Vcf ] repr

val varscan_somatic : ?adjust_mapq:int ->
       normal:[ `Bam ] repr -> tumor:[ `Bam ] repr -> unit -> [ `Vcf ] repr

val strelka : ?configuration:Biokepi_bfx_tools.Strelka.Configuration.t ->
       normal:[ `Bam ] repr -> tumor:[ `Bam ] repr -> unit -> [ `Vcf ] repr

val virmid : ?configuration:Biokepi_bfx_tools.Virmid.Configuration.t ->
       normal:[ `Bam ] repr -> tumor:[ `Bam ] repr -> unit -> [ `Vcf ] repr

val muse : ?configuration:Biokepi_bfx_tools.Muse.Configuration.t ->
       normal:[ `Bam ] repr -> tumor:[ `Bam ] repr -> unit -> [ `Vcf ] repr