Module Biokepi_pipeline_edsl.Pipeline.Construct (.ml)

module Construct: sig .. end

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 ->
       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 : [ `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