Module Biokepi_bfx_tools.Bwa (.ml)

module Bwa: sig .. end

module Remove: Biokepi_run_environment.Workflow_utilities.Remove

module Configuration: sig .. end

val index : reference_build:string ->
       run_with:Biokepi_run_environment.Machine.t ->
       < 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 read_group_header_option : [< `Aln | `Mem ] -> sample_name:string -> read_group_id:string -> string

val mem_align_to_sam : reference_build:string ->
       ?configuration:Configuration.Mem.t ->
       fastq:< escaped_sample_name : string;
               is_done : Biokepi_run_environment.Common.KEDSL.Condition.t option;
               paths : string * string option; .. >
             Biokepi_run_environment.Common.KEDSL.workflow_node ->
       result_prefix:string ->
       run_with:Biokepi_run_environment.Machine.t ->
       unit ->
       < 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 align_to_sam : reference_build:string ->
       ?configuration:Configuration.Aln.t ->
       fastq:< escaped_sample_name : string;
               is_done : Biokepi_run_environment.Common.KEDSL.Condition.t option;
               paths : string * string option; .. >
             Biokepi_run_environment.Common.KEDSL.workflow_node ->
       result_prefix:string ->
       run_with:Biokepi_run_environment.Machine.t ->
       unit ->
       < 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 Input_reads: sig .. end

val mem_align_to_bam : reference_build:string ->
       ?configuration:Configuration.Mem.t ->
       result_prefix:string ->
       run_with:Biokepi_run_environment.Machine.t ->
       Input_reads.t ->
       < 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