Module Biokepi_bfx_tools.Gatk (.ml)

module Gatk: sig .. end

module Remove: Biokepi_run_environment.Workflow_utilities.Remove

module Configuration: sig .. end

val indel_realigner_output_filename_tag : configuration:Configuration.Indel_realigner.t *
                     Configuration.Realigner_target_creator.t ->
       ?region:[< `Chromosome of string
                | `Chromosome_interval of string * int * int
                | `Full ] ->
       < product : < path : string; .. >; .. > list -> string

val indel_realigner : 'a.
         ?compress:bool ->
         ?on_region:Biokepi_run_environment.Region.t ->
         configuration:Configuration.Indel_realigner.t *
                       Configuration.Realigner_target_creator.t ->
         run_with:Biokepi_run_environment.Machine.t ->
         ?run_directory:string ->
         'a Biokepi_run_environment.Common.KEDSL.bam_or_bams -> 'a

val indel_realigner_map_reduce : 'a.
         ?compress:bool ->
         configuration:Configuration.Indel_realigner.t *
                       Configuration.Realigner_target_creator.t ->
         run_with:Biokepi_run_environment.Machine.t ->
         ?run_directory:string ->
         'a Biokepi_run_environment.Common.KEDSL.bam_or_bams -> 'a

val call_gatk : analysis:string ->
       ?region:[< `Chromosome of string
                | `Chromosome_interval of string * int * int
                | `Full
                > `Full ] ->
       string list -> Biokepi_run_environment.Common.KEDSL.Program.t

val base_quality_score_recalibrator : configuration:Configuration.Bqsr.t *
                     Configuration.Print_reads.t ->
       run_with:Biokepi_run_environment.Machine.t ->
       input_bam:Biokepi_run_environment.Common.KEDSL.bam_file
                 Biokepi_run_environment.Common.KEDSL.workflow_node ->
       output_bam:string ->
       < escaped_sample_name : string;
         host : Biokepi_run_environment.Common.KEDSL.Host.t;
         is_done : Biokepi_run_environment.Common.KEDSL.Condition.t option;
         path : string; reference_build : string; sample_name : string;
         sorting : [ `Coordinate | `Read_name ] option >
       Biokepi_run_environment.Common.KEDSL.workflow_node

val haplotype_caller : ?more_edges:Biokepi_run_environment.Common.KEDSL.workflow_edge list ->
       run_with:Biokepi_run_environment.Machine.t ->
       input_bam:Biokepi_run_environment.Common.KEDSL.bam_file
                 Biokepi_run_environment.Common.KEDSL.workflow_node ->
       result_prefix:string ->
       [< `Map_reduce
        | `Region of
            [< `Chromosome of string
             | `Chromosome_interval of string * int * int
             | `Full
             > `Full ] ] ->
       < as_single_file : Biokepi_run_environment.Common.KEDSL.single_file
                          Biokepi_run_environment.Common.KEDSL.product;
         host : Biokepi_run_environment.Common.KEDSL.Host.t;
         is_done : Biokepi_run_environment.Common.KEDSL.Condition.t option;
         path : string; reference_build : string >
       Biokepi_run_environment.Common.KEDSL.workflow_node

val mutect2 : ?more_edges:Biokepi_run_environment.Common.KEDSL.workflow_edge list ->
       configuration:Configuration.Mutect2.t ->
       run_with:Biokepi_run_environment.Machine.t ->
       input_normal_bam:Biokepi_run_environment.Common.KEDSL.bam_file
                        Biokepi_run_environment.Common.KEDSL.workflow_node ->
       input_tumor_bam:Biokepi_run_environment.Common.KEDSL.bam_file
                       Biokepi_run_environment.Common.KEDSL.workflow_node ->
       result_prefix:string ->
       [< `Map_reduce
        | `Region of
            [< `Chromosome of string
             | `Chromosome_interval of string * int * int
             | `Full
             > `Full ] ] ->
       < as_single_file : Biokepi_run_environment.Common.KEDSL.single_file
                          Biokepi_run_environment.Common.KEDSL.product;
         host : Biokepi_run_environment.Common.KEDSL.Host.t;
         is_done : Biokepi_run_environment.Common.KEDSL.Condition.t option;
         path : string; reference_build : string >
       Biokepi_run_environment.Common.KEDSL.workflow_node