Module Biokepi_pipeline_edsl.Pipeline.Compiler (.ml)

module Compiler: sig .. end

type 'a pipeline = 'a Biokepi_pipeline_edsl.Pipeline.t 

type workflow_option_failure_mode = [ `Fail_if_not_happening | `Silent ] 

type workflow_option = [ `Map_reduce of [ `Gatk_indel_realigner ]
       | `Multi_sample_indel_realignment of
           workflow_option_failure_mode
       | `Parallel_alignment_over_fastq_fragments of
           [ `Bwa | `Bwa_mem | `Hisat | `Mosaik | `Star ] list *
           workflow_option_failure_mode ] 

type t = {

val create : ?wrap_bam_node:(Biokepi_pipeline_edsl.Pipeline.bam
                       pipeline ->
                       Biokepi_run_environment.Common.KEDSL.bam_file
                       Biokepi_run_environment.Common.KEDSL.workflow_node ->
                       Biokepi_run_environment.Common.KEDSL.bam_file
                       Biokepi_run_environment.Common.KEDSL.workflow_node) ->
       ?wrap_vcf_node:(Biokepi_pipeline_edsl.Pipeline.vcf
                       pipeline ->
                       Biokepi_run_environment.Common.KEDSL.vcf_file
                       Biokepi_run_environment.Common.KEDSL.workflow_node ->
                       Biokepi_run_environment.Common.KEDSL.vcf_file
                       Biokepi_run_environment.Common.KEDSL.workflow_node) ->
       ?wrap_gtf_node:(Biokepi_pipeline_edsl.Pipeline.gtf
                       pipeline ->
                       Biokepi_run_environment.Common.KEDSL.single_file
                       Biokepi_run_environment.Common.KEDSL.workflow_node ->
                       Biokepi_run_environment.Common.KEDSL.single_file
                       Biokepi_run_environment.Common.KEDSL.workflow_node) ->
       ?options:workflow_option list ->
       reference_build:Biokepi_run_environment.Reference_genome.name ->
       work_dir:string ->
       machine:Biokepi_run_environment.Machine.t ->
       unit -> t

val has_option : t ->
       (workflow_option -> bool) -> bool

val apply_with_metadata : metadata_spec:[< `Add_tags of string list | `Add_tags_rec of string list ] ->
       (< is_done : Biokepi_run_environment.Common.KEDSL.Condition.t option; .. >
        as 'a)
       Biokepi_run_environment.Common.KEDSL.product
       Biokepi_run_environment.Common.KEDSL.workflow_node ->
       'a Biokepi_run_environment.Common.KEDSL.product
       Biokepi_run_environment.Common.KEDSL.workflow_node

val fastq_step : read:[ `R1 of string | `R2 of string ] ->
       compiler:t ->
       Biokepi_pipeline_edsl.Pipeline.fastq
       pipeline ->
       Biokepi_pipeline_edsl.Pipeline.File.t

val fastq_sample_step : compiler:t ->
       Biokepi_pipeline_edsl.Pipeline.fastq_sample
       pipeline ->
       < 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.product
       Biokepi_run_environment.Common.KEDSL.workflow_node

val compile_aligner_step : compiler:t ->
       Biokepi_pipeline_edsl.Pipeline.bam
       pipeline ->
       Biokepi_run_environment.Common.KEDSL.bam_file
       Biokepi_run_environment.Common.KEDSL.workflow_node

val compile_bam_pair : compiler:t ->
       Biokepi_pipeline_edsl.Pipeline.bam_pair
       pipeline ->
       [ `Normal of
           Biokepi_run_environment.Common.KEDSL.bam_file
           Biokepi_run_environment.Common.KEDSL.workflow_node ] *
       [ `Tumor of
           Biokepi_run_environment.Common.KEDSL.bam_file
           Biokepi_run_environment.Common.KEDSL.workflow_node ] *
       [ `Pipeline of
           Biokepi_pipeline_edsl.Pipeline.bam_pair
           pipeline ]

val compile_variant_caller_step : compiler:t ->
       Biokepi_pipeline_edsl.Pipeline.vcf
       pipeline ->
       Biokepi_run_environment.Common.KEDSL.vcf_file
       Biokepi_run_environment.Common.KEDSL.product
       Biokepi_run_environment.Common.KEDSL.product
       Biokepi_run_environment.Common.KEDSL.workflow_node

val compile_gtf_step : compiler:t ->
       Biokepi_pipeline_edsl.Pipeline.gtf
       pipeline ->
       < 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.product
       Biokepi_run_environment.Common.KEDSL.product
       Biokepi_run_environment.Common.KEDSL.workflow_node

val seq2hla_hla_types_step : compiler:t ->
       Biokepi_pipeline_edsl.Pipeline.seq2hla_hla_types
       pipeline ->
       Biokepi_bfx_tools.Seq2HLA.product
       Biokepi_run_environment.Common.KEDSL.workflow_node

val optitype_hla_types_step : compiler:t ->
       Biokepi_pipeline_edsl.Pipeline.optitype_hla_types
       pipeline ->
       Biokepi_bfx_tools.Optitype.product
       Biokepi_run_environment.Common.KEDSL.workflow_node