sig
module Remove = Biokepi_run_environment.Workflow_utilities.Remove
module Configuration :
sig
module Gatk_config :
functor () ->
sig
type t = {
name : string;
filter_reads_with_n_cigar : bool;
filter_mismatching_base_and_quals : bool;
filter_bases_not_stored : bool;
parameters : (string * string) list;
}
val name :
Biokepi_bfx_tools.Gatk.Configuration.Gatk_config.t -> string
val to_json :
Biokepi_bfx_tools.Gatk.Configuration.Gatk_config.t ->
Yojson.Basic.json
val render :
Biokepi_bfx_tools.Gatk.Configuration.Gatk_config.t ->
string list
val default : Biokepi_bfx_tools.Gatk.Configuration.Gatk_config.t
end
module Indel_realigner :
sig
type t = {
name : string;
filter_reads_with_n_cigar : bool;
filter_mismatching_base_and_quals : bool;
filter_bases_not_stored : bool;
parameters : (string * string) list;
}
val name : t -> string
val to_json : t -> Yojson.Basic.json
val render : t -> string list
val default : t
end
module Realigner_target_creator :
sig
type t = {
name : string;
filter_reads_with_n_cigar : bool;
filter_mismatching_base_and_quals : bool;
filter_bases_not_stored : bool;
parameters : (string * string) list;
}
val name : t -> string
val to_json : t -> Yojson.Basic.json
val render : t -> string list
val default : t
end
module Bqsr :
sig
type t = {
name : string;
filter_reads_with_n_cigar : bool;
filter_mismatching_base_and_quals : bool;
filter_bases_not_stored : bool;
parameters : (string * string) list;
}
val name : t -> string
val to_json : t -> Yojson.Basic.json
val render : t -> string list
val default : t
end
module Print_reads :
sig
type t = {
name : string;
filter_reads_with_n_cigar : bool;
filter_mismatching_base_and_quals : bool;
filter_bases_not_stored : bool;
parameters : (string * string) list;
}
val name : t -> string
val to_json : t -> Yojson.Basic.json
val render : t -> string list
val default : t
end
type indel_realigner =
Biokepi_bfx_tools.Gatk.Configuration.Indel_realigner.t *
Biokepi_bfx_tools.Gatk.Configuration.Realigner_target_creator.t
type bqsr =
Biokepi_bfx_tools.Gatk.Configuration.Bqsr.t *
Biokepi_bfx_tools.Gatk.Configuration.Print_reads.t
val default_indel_realigner :
Biokepi_bfx_tools.Gatk.Configuration.Indel_realigner.t *
Biokepi_bfx_tools.Gatk.Configuration.Realigner_target_creator.t
val default_bqsr :
Biokepi_bfx_tools.Gatk.Configuration.Bqsr.t *
Biokepi_bfx_tools.Gatk.Configuration.Print_reads.t
module Mutect2 :
sig
type t = {
name : string;
use_dbsnp : bool;
use_cosmic : bool;
additional_arguments : string list;
}
val create :
?use_dbsnp:bool ->
?use_cosmic:bool ->
string ->
string list -> Biokepi_bfx_tools.Gatk.Configuration.Mutect2.t
val to_json :
Biokepi_bfx_tools.Gatk.Configuration.Mutect2.t ->
Yojson.Basic.json
val default : Biokepi_bfx_tools.Gatk.Configuration.Mutect2.t
val default_without_cosmic :
Biokepi_bfx_tools.Gatk.Configuration.Mutect2.t
val compile :
reference:Biokepi_run_environment.Reference_genome.t ->
Biokepi_bfx_tools.Gatk.Configuration.Mutect2.t ->
[> `Arguments of string list ] *
[> `Edges of
Biokepi_run_environment.Common.KEDSL.workflow_edge list ]
val name : Biokepi_bfx_tools.Gatk.Configuration.Mutect2.t -> string
end
end
val indel_realigner_output_filename_tag :
configuration:Biokepi_bfx_tools.Gatk.Configuration.Indel_realigner.t *
Biokepi_bfx_tools.Gatk.Configuration.Realigner_target_creator.t ->
?region:[< `Chromosome of string
| `Chromosome_interval of string * int * int
| `Full ] ->
< product : < path : string; .. >; .. > list -> string
val indel_realigner :
?compress:bool ->
?on_region:Biokepi_run_environment.Region.t ->
configuration:Biokepi_bfx_tools.Gatk.Configuration.Indel_realigner.t *
Biokepi_bfx_tools.Gatk.Configuration.Realigner_target_creator.t ->
run_with:Biokepi_run_environment.Machine.t ->
?run_directory:string ->
'a Biokepi_run_environment.Common.KEDSL.bam_or_bams -> 'a
val indel_realigner_map_reduce :
?compress:bool ->
configuration:Biokepi_bfx_tools.Gatk.Configuration.Indel_realigner.t *
Biokepi_bfx_tools.Gatk.Configuration.Realigner_target_creator.t ->
run_with:Biokepi_run_environment.Machine.t ->
?run_directory:string ->
'a Biokepi_run_environment.Common.KEDSL.bam_or_bams -> 'a
val call_gatk :
analysis:string ->
?region:[< `Chromosome of string
| `Chromosome_interval of string * int * int
| `Full
> `Full ] ->
string list -> Biokepi_run_environment.Common.KEDSL.Program.t
val base_quality_score_recalibrator :
configuration:Biokepi_bfx_tools.Gatk.Configuration.Bqsr.t *
Biokepi_bfx_tools.Gatk.Configuration.Print_reads.t ->
run_with:Biokepi_run_environment.Machine.t ->
input_bam:Biokepi_run_environment.Common.KEDSL.bam_file
Biokepi_run_environment.Common.KEDSL.workflow_node ->
output_bam:string ->
< 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
val haplotype_caller :
?more_edges:Biokepi_run_environment.Common.KEDSL.workflow_edge list ->
run_with:Biokepi_run_environment.Machine.t ->
input_bam:Biokepi_run_environment.Common.KEDSL.bam_file
Biokepi_run_environment.Common.KEDSL.workflow_node ->
result_prefix:string ->
[< `Map_reduce
| `Region of
[< `Chromosome of string
| `Chromosome_interval of string * int * int
| `Full
> `Full ] ] ->
< 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
val mutect2 :
?more_edges:Biokepi_run_environment.Common.KEDSL.workflow_edge list ->
configuration:Biokepi_bfx_tools.Gatk.Configuration.Mutect2.t ->
run_with:Biokepi_run_environment.Machine.t ->
input_normal_bam:Biokepi_run_environment.Common.KEDSL.bam_file
Biokepi_run_environment.Common.KEDSL.workflow_node ->
input_tumor_bam:Biokepi_run_environment.Common.KEDSL.bam_file
Biokepi_run_environment.Common.KEDSL.workflow_node ->
result_prefix:string ->
[< `Map_reduce
| `Region of
[< `Chromosome of string
| `Chromosome_interval of string * int * int
| `Full
> `Full ] ] ->
< 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
end