sig
module Remove = Biokepi_run_environment.Workflow_utilities.Remove
module Configuration :
sig
type t = {
name : string;
with_cosmic : bool;
with_dbsnp : bool;
parameters : (string * string) list;
}
val to_json :
Biokepi_bfx_tools.Mutect.Configuration.t -> Yojson.Basic.json
val render : Biokepi_bfx_tools.Mutect.Configuration.t -> string list
val default : Biokepi_bfx_tools.Mutect.Configuration.t
val default_without_cosmic : Biokepi_bfx_tools.Mutect.Configuration.t
val name : Biokepi_bfx_tools.Mutect.Configuration.t -> string
end
val run :
run_with:Biokepi_run_environment.Machine.t ->
normal:Biokepi_run_environment.Common.KEDSL.bam_file
Biokepi_run_environment.Common.KEDSL.workflow_node ->
tumor:Biokepi_run_environment.Common.KEDSL.bam_file
Biokepi_run_environment.Common.KEDSL.workflow_node ->
result_prefix:string ->
?more_edges:Biokepi_run_environment.Common.KEDSL.workflow_edge list ->
configuration:Biokepi_bfx_tools.Mutect.Configuration.t ->
[< `Map_reduce
| `Region of
[< `Chromosome of string
| `Chromosome_interval of string * int * int
| `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