sig
module Remove = Biokepi_run_environment.Workflow_utilities.Remove
module Configuration :
sig
module Common_config :
sig
type t = {
name : string;
gap_open_penalty : int;
gap_extension_penalty : int;
mismatch_penalty : int;
}
end
module Bwa_config :
functor
(D : sig
val default :
Biokepi_bfx_tools.Bwa.Configuration.Common_config.t
end) ->
sig
type t =
Common_config.t = {
name : string;
gap_open_penalty : int;
gap_extension_penalty : int;
mismatch_penalty : int;
}
val name : t -> string
val default : Biokepi_bfx_tools.Bwa.Configuration.Common_config.t
val to_json :
t ->
[> `Assoc of
(string * [> `Int of int | `String of string ]) list ]
end
val bwa_mem_default :
Biokepi_bfx_tools.Bwa.Configuration.Common_config.t
module Mem :
sig
type t =
Common_config.t = {
name : string;
gap_open_penalty : int;
gap_extension_penalty : int;
mismatch_penalty : int;
}
val name : t -> string
val default : Common_config.t
val to_json :
t ->
[> `Assoc of (string * [> `Int of int | `String of string ]) list ]
end
val bwa_aln_default :
Biokepi_bfx_tools.Bwa.Configuration.Common_config.t
module Aln :
sig
type t =
Common_config.t = {
name : string;
gap_open_penalty : int;
gap_extension_penalty : int;
mismatch_penalty : int;
}
val name : t -> string
val default : Common_config.t
val to_json :
t ->
[> `Assoc of (string * [> `Int of int | `String of string ]) list ]
end
end
val index :
reference_build:string ->
run_with:Biokepi_run_environment.Machine.t ->
< 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.workflow_node
val read_group_header_option :
[< `Aln | `Mem ] -> sample_name:string -> read_group_id:string -> string
val mem_align_to_sam :
reference_build:string ->
?configuration:Biokepi_bfx_tools.Bwa.Configuration.Mem.t ->
fastq:< escaped_sample_name : string;
is_done : Biokepi_run_environment.Common.KEDSL.Condition.t option;
paths : string * string option; .. >
Biokepi_run_environment.Common.KEDSL.workflow_node ->
result_prefix:string ->
run_with:Biokepi_run_environment.Machine.t ->
unit ->
< 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.workflow_node
val align_to_sam :
reference_build:string ->
?configuration:Biokepi_bfx_tools.Bwa.Configuration.Aln.t ->
fastq:< escaped_sample_name : string;
is_done : Biokepi_run_environment.Common.KEDSL.Condition.t option;
paths : string * string option; .. >
Biokepi_run_environment.Common.KEDSL.workflow_node ->
result_prefix:string ->
run_with:Biokepi_run_environment.Machine.t ->
unit ->
< 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.workflow_node
module Input_reads :
sig
type t =
[ `Bam of
Biokepi_run_environment.Common.KEDSL.bam_file
Biokepi_run_environment.Common.KEDSL.workflow_node *
[ `PE | `SE ]
| `Fastq of
Biokepi_run_environment.Common.KEDSL.fastq_reads
Biokepi_run_environment.Common.KEDSL.workflow_node ]
val prepare :
run_with:Biokepi_run_environment.Machine.t ->
[< `Bam of
Biokepi_run_environment.Common.KEDSL.bam_file
Biokepi_run_environment.Common.KEDSL.workflow_node * 'a
| `Fastq of 'b ] ->
[> `Bam of
Biokepi_run_environment.Common.KEDSL.bam_file
Biokepi_run_environment.Common.KEDSL.workflow_node * 'a
| `Fastq of 'b ]
val name :
[< `Bam of < product : < path : string; .. >; .. > * 'a
| `Fastq of < product : < paths : string * 'b; .. >; .. > ] ->
string
val sample_name :
[< `Bam of < product : < escaped_sample_name : 'a; .. >; .. > * 'b
| `Fastq of < product : < escaped_sample_name : 'a; .. >; .. > ] ->
'a
val read_group_id :
[< `Bam of < product : < path : string; .. >; .. > * 'a
| `Fastq of < product : < paths : string * 'b; .. >; .. > ] ->
string
val as_dependencies :
[< `Bam of
< is_done : Biokepi_run_environment.Common.KEDSL.Condition.t
option;
.. >
Biokepi_run_environment.Common.KEDSL.workflow_node * 'a
| `Fastq of
< is_done : Biokepi_run_environment.Common.KEDSL.Condition.t
option;
.. >
Biokepi_run_environment.Common.KEDSL.workflow_node ] ->
Biokepi_run_environment.Common.KEDSL.workflow_edge list
end
val mem_align_to_bam :
reference_build:string ->
?configuration:Biokepi_bfx_tools.Bwa.Configuration.Mem.t ->
result_prefix:string ->
run_with:Biokepi_run_environment.Machine.t ->
Biokepi_bfx_tools.Bwa.Input_reads.t ->
< 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
end