Module Biokepi_bfx_tools.Picard (.ml)

module Picard: sig .. end

module Remove: Biokepi_run_environment.Workflow_utilities.Remove

val create_dict : run_with:Biokepi_run_environment.Machine.t ->
       < is_done : Biokepi_run_environment.Common.KEDSL.Condition.t option;
         path : string; .. >
       Biokepi_run_environment.Common.KEDSL.workflow_node ->
       < exists : Ketrew_pure.Target.Condition.t;
         host : Biokepi_run_environment.Common.KEDSL.Host.t;
         is_bigger_than : int -> Ketrew_pure.Target.Condition.t;
         is_done : Biokepi_run_environment.Common.KEDSL.Condition.t option;
         path : string >
       Biokepi_run_environment.Common.KEDSL.workflow_node

val sort_vcf : run_with:Biokepi_run_environment.Machine.t ->
       ?sequence_dict:< is_done : Biokepi_run_environment.Common.KEDSL.Condition.t
                                  option;
                        path : string; .. >
                      Biokepi_run_environment.Common.KEDSL.workflow_node ->
       < is_done : Biokepi_run_environment.Common.KEDSL.Condition.t option;
         path : string; .. >
       Biokepi_run_environment.Common.KEDSL.workflow_node ->
       < exists : Ketrew_pure.Target.Condition.t;
         host : Biokepi_run_environment.Common.KEDSL.Host.t;
         is_bigger_than : int -> Ketrew_pure.Target.Condition.t;
         is_done : Biokepi_run_environment.Common.KEDSL.Condition.t option;
         path : string >
       Biokepi_run_environment.Common.KEDSL.workflow_node

module Mark_duplicates_settings: sig .. end

val mark_duplicates : ?settings:Mark_duplicates_settings.t ->
       run_with:Biokepi_run_environment.Machine.t ->
       input_bam:Biokepi_run_environment.Common.KEDSL.bam_file
                 Biokepi_run_environment.Common.KEDSL.workflow_node ->
       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 reorder_sam : run_with:Biokepi_run_environment.Machine.t ->
       ?mem_param:string ->
       ?reference_build:string ->
       input_bam:< is_done : Biokepi_run_environment.Common.KEDSL.Condition.t option;
                   path : string; reference_build : string; .. >
                 Biokepi_run_environment.Common.KEDSL.workflow_node ->
       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 bam_to_fastq : run_with:Biokepi_run_environment.Machine.t ->
       sample_type:[< `Paired_end | `Single_end ] ->
       output_prefix:string ->
       Biokepi_run_environment.Common.KEDSL.bam_file
       Biokepi_run_environment.Common.KEDSL.workflow_node ->
       < escaped_sample_name : string; fragment_id : string option;
         fragment_id_forced : string;
         is_done : Biokepi_run_environment.Common.KEDSL.Condition.t option;
         paths : string * string option;
         r1 : Biokepi_run_environment.Common.KEDSL.single_file;
         r2 : Biokepi_run_environment.Common.KEDSL.single_file option;
         sample_name : string >
       Biokepi_run_environment.Common.KEDSL.workflow_node

val clean_bam : run_with:Biokepi_run_environment.Machine.t ->
       Biokepi_run_environment.Common.KEDSL.bam_file
       Biokepi_run_environment.Common.KEDSL.workflow_node ->
       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