sig
module Remove = Biokepi_run_environment.Workflow_utilities.Remove
val create_dict :
run_with:Biokepi_run_environment.Machine.t ->
< is_done : Biokepi_run_environment.Common.KEDSL.Condition.t option;
path : string; .. >
Biokepi_run_environment.Common.KEDSL.workflow_node ->
< 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 sort_vcf :
run_with:Biokepi_run_environment.Machine.t ->
?sequence_dict:< is_done : Biokepi_run_environment.Common.KEDSL.Condition.t
option;
path : string; .. >
Biokepi_run_environment.Common.KEDSL.workflow_node ->
< is_done : Biokepi_run_environment.Common.KEDSL.Condition.t option;
path : string; .. >
Biokepi_run_environment.Common.KEDSL.workflow_node ->
< 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 Mark_duplicates_settings :
sig
type t = {
name : string;
tmpdir : string option;
max_sequences_for_disk_read_ends_map : int;
max_file_handles_for_read_ends_map : int;
sorting_collection_size_ratio : float;
mem_param : string option;
}
val factory : Biokepi_bfx_tools.Picard.Mark_duplicates_settings.t
val default : Biokepi_bfx_tools.Picard.Mark_duplicates_settings.t
val to_java_shell_call :
default_tmp_dir:string ->
Biokepi_bfx_tools.Picard.Mark_duplicates_settings.t -> string
end
val mark_duplicates :
?settings:Biokepi_bfx_tools.Picard.Mark_duplicates_settings.t ->
run_with:Biokepi_run_environment.Machine.t ->
input_bam:Biokepi_run_environment.Common.KEDSL.bam_file
Biokepi_run_environment.Common.KEDSL.workflow_node ->
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 reorder_sam :
run_with:Biokepi_run_environment.Machine.t ->
?mem_param:string ->
?reference_build:string ->
input_bam:< is_done : Biokepi_run_environment.Common.KEDSL.Condition.t
option;
path : string; reference_build : string; .. >
Biokepi_run_environment.Common.KEDSL.workflow_node ->
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 bam_to_fastq :
run_with:Biokepi_run_environment.Machine.t ->
sample_type:[< `Paired_end | `Single_end ] ->
output_prefix:string ->
Biokepi_run_environment.Common.KEDSL.bam_file
Biokepi_run_environment.Common.KEDSL.workflow_node ->
< escaped_sample_name : string; fragment_id : string option;
fragment_id_forced : string;
is_done : Biokepi_run_environment.Common.KEDSL.Condition.t option;
paths : string * string option;
r1 : Biokepi_run_environment.Common.KEDSL.single_file;
r2 : Biokepi_run_environment.Common.KEDSL.single_file option;
sample_name : string >
Biokepi_run_environment.Common.KEDSL.workflow_node
val clean_bam :
run_with:Biokepi_run_environment.Machine.t ->
Biokepi_run_environment.Common.KEDSL.bam_file
Biokepi_run_environment.Common.KEDSL.workflow_node ->
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
end