Module Biokepi_run_environment.Workflow_utilities.Vcftools (.ml)

module Vcftools: sig .. end

val vcf_process_n_to_1_no_machine : host:Common.KEDSL.Host.t ->
       vcftools:Biokepi_run_environment.Machine.Tool.t ->
       run_program:Biokepi_run_environment.Machine.Make_fun.t ->
       ?more_edges:Biokepi_run_environment.Common.KEDSL.workflow_edge list ->
       vcfs:< is_done : Common.KEDSL.Condition.t option; path : string; .. >
            Biokepi_run_environment.Common.KEDSL.workflow_node list ->
       make_product:(string ->
                     (< is_done : Common.KEDSL.Condition.t option; .. > as 'a)
                     Biokepi_run_environment.Common.KEDSL.product) ->
       final_vcf:string ->
       string -> 'a Biokepi_run_environment.Common.KEDSL.workflow_node

Call a command on a list of ~vcfs to produce a given ~final_vcf (hence the n-to-1 naming).

val vcf_concat_no_machine : host:Common.KEDSL.Host.t ->
       vcftools:Biokepi_run_environment.Machine.Tool.t ->
       run_program:Biokepi_run_environment.Machine.Make_fun.t ->
       ?more_edges:Biokepi_run_environment.Common.KEDSL.workflow_edge list ->
       make_product:(string ->
                     (< is_done : Common.KEDSL.Condition.t option; .. > as 'a)
                     Biokepi_run_environment.Common.KEDSL.product) ->
       < is_done : Common.KEDSL.Condition.t option; path : string; .. >
       Biokepi_run_environment.Common.KEDSL.workflow_node list ->
       final_vcf:string -> 'a Biokepi_run_environment.Common.KEDSL.workflow_node

Concatenate VCF files.

We use this version where we don't yet have a Machine.t, as in "download_reference_genome.ml".

val vcf_sort_no_machine : host:Common.KEDSL.Host.t ->
       vcftools:Biokepi_run_environment.Machine.Tool.t ->
       run_program:Biokepi_run_environment.Machine.Make_fun.t ->
       ?more_edges:Biokepi_run_environment.Common.KEDSL.workflow_edge list ->
       make_product:(string ->
                     (< is_done : Common.KEDSL.Condition.t option; .. > as 'a)
                     Biokepi_run_environment.Common.KEDSL.product) ->
       src:< is_done : Common.KEDSL.Condition.t option; path : string; .. >
           Biokepi_run_environment.Common.KEDSL.workflow_node ->
       dest:string -> unit -> 'a Biokepi_run_environment.Common.KEDSL.workflow_node

Sort a VCF file by choromosome position (it uses "vcf-sort" which itself relies on the "sort" unix tool having the "--version-sort" option).

We use this version where we don't yet have a Machine.t, as in "download_reference_genome.ml".