sig
module Definition :
sig
type t = { name : string; version : string option; }
val create :
?version:string ->
string -> Biokepi_run_environment.Machine.Tool.Definition.t
val to_opam_name :
Biokepi_run_environment.Machine.Tool.Definition.t -> string
val to_string :
Biokepi_run_environment.Machine.Tool.Definition.t -> string
val to_directory_name :
Biokepi_run_environment.Machine.Tool.Definition.t -> string
val get_version :
Biokepi_run_environment.Machine.Tool.Definition.t -> string option
val get_name :
Biokepi_run_environment.Machine.Tool.Definition.t -> string
end
module Default :
sig
val bwa : Biokepi_run_environment.Machine.Tool.Definition.t
val freebayes : Biokepi_run_environment.Machine.Tool.Definition.t
val sambamba : Biokepi_run_environment.Machine.Tool.Definition.t
val samtools : Biokepi_run_environment.Machine.Tool.Definition.t
val bcftools : Biokepi_run_environment.Machine.Tool.Definition.t
val vcftools : Biokepi_run_environment.Machine.Tool.Definition.t
val bedtools : Biokepi_run_environment.Machine.Tool.Definition.t
val somaticsniper : Biokepi_run_environment.Machine.Tool.Definition.t
val varscan : Biokepi_run_environment.Machine.Tool.Definition.t
val mutect : Biokepi_run_environment.Machine.Tool.Definition.t
val gatk : Biokepi_run_environment.Machine.Tool.Definition.t
val strelka : Biokepi_run_environment.Machine.Tool.Definition.t
val virmid : Biokepi_run_environment.Machine.Tool.Definition.t
val muse : Biokepi_run_environment.Machine.Tool.Definition.t
val star : Biokepi_run_environment.Machine.Tool.Definition.t
val stringtie : Biokepi_run_environment.Machine.Tool.Definition.t
val cufflinks : Biokepi_run_environment.Machine.Tool.Definition.t
val hisat : Biokepi_run_environment.Machine.Tool.Definition.t
val hisat2 : Biokepi_run_environment.Machine.Tool.Definition.t
val mosaik : Biokepi_run_environment.Machine.Tool.Definition.t
val kallisto : Biokepi_run_environment.Machine.Tool.Definition.t
val bowtie : Biokepi_run_environment.Machine.Tool.Definition.t
val fastqc : Biokepi_run_environment.Machine.Tool.Definition.t
val igvxml : Biokepi_run_environment.Machine.Tool.Definition.t
val hlarp : Biokepi_run_environment.Machine.Tool.Definition.t
val samblaster : Biokepi_run_environment.Machine.Tool.Definition.t
val delly2 : Biokepi_run_environment.Machine.Tool.Definition.t
val optitype : Biokepi_run_environment.Machine.Tool.Definition.t
val seqtk : Biokepi_run_environment.Machine.Tool.Definition.t
val seq2hla : Biokepi_run_environment.Machine.Tool.Definition.t
val picard : Biokepi_run_environment.Machine.Tool.Definition.t
val snpeff : Biokepi_run_environment.Machine.Tool.Definition.t
val pyensembl : Biokepi_run_environment.Machine.Tool.Definition.t
val vcfannotatepolyphen :
Biokepi_run_environment.Machine.Tool.Definition.t
val topiary : Biokepi_run_environment.Machine.Tool.Definition.t
val vaxrank : Biokepi_run_environment.Machine.Tool.Definition.t
val isovar : Biokepi_run_environment.Machine.Tool.Definition.t
end
type t = {
definition : Biokepi_run_environment.Machine.Tool.Definition.t;
init : Common.KEDSL.Program.t;
ensure : Biokepi_run_environment.Common.KEDSL.phony_workflow;
}
val create :
?init:Common.KEDSL.Program.t ->
?ensure:< is_done : Common.KEDSL.Condition.t option; .. >
Biokepi_run_environment.Common.KEDSL.workflow_node ->
Biokepi_run_environment.Machine.Tool.Definition.t ->
Biokepi_run_environment.Machine.Tool.t
val init : Biokepi_run_environment.Machine.Tool.t -> Common.KEDSL.Program.t
val ensure :
Biokepi_run_environment.Machine.Tool.t ->
Biokepi_run_environment.Common.KEDSL.phony_workflow
module Kit :
sig
type tool = Biokepi_run_environment.Machine.Tool.t
type t =
Biokepi_run_environment.Machine.Tool.Definition.t ->
Biokepi_run_environment.Machine.Tool.Kit.tool option
val concat :
Biokepi_run_environment.Machine.Tool.Kit.t list ->
Biokepi_run_environment.Machine.Tool.Kit.t
val of_list :
Biokepi_run_environment.Machine.Tool.Kit.tool list ->
Biokepi_run_environment.Machine.Tool.Kit.t
val get_exn :
(Biokepi_run_environment.Machine.Tool.Definition.t -> 'a option) ->
Biokepi_run_environment.Machine.Tool.Definition.t -> 'a
end
end