Module Biokepi_bfx_tools.Bedtools (.ml)

module Bedtools: sig .. end

module Remove: Biokepi_run_environment.Workflow_utilities.Remove

module Configuration: sig .. end

val bamtofastq : 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 intersect : run_with:Biokepi_run_environment.Machine.t ->
       ?configuration:Configuration.Intersect.t ->
       primary:< 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 ->
       intersect_with:< is_done : Biokepi_run_environment.Common.KEDSL.Condition.t
                                  option;
                        path : string; .. >
                      Biokepi_run_environment.Common.KEDSL.workflow_node list ->
       string ->
       < 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