struct
open Biokepi_run_environment
open Common
module Remove = Workflow_utilities.Remove
module Configuration = struct
type t = {
name: string;
input_type: [ `WGS | `WES ];
}
let name t = t.name
let input_type_to_string input_type =
match input_type with
| `WGS -> "WGS"
| `WES -> "WES"
let to_json {name; input_type} =
`Assoc [
"name", `String name;
"input-type", `String (input_type_to_string input_type);
]
let default input_type =
let is = input_type_to_string input_type in
{ name = "default-" ^ is; input_type}
let wgs = default `WGS
let wes = default `WES
end
let run
~configuration
~(run_with:Machine.t) ~normal ~tumor ~result_prefix ?(more_edges = []) how =
let open KEDSL in
let reference =
Machine.get_reference_genome run_with normal#product#reference_build in
let muse_tool = Machine.get_tool run_with Machine.Tool.Default.muse in
let muse_call_on_region region =
let result_file suffix =
let region_name = Region.to_filename region in
sprintf "%s-%s%s" result_prefix region_name suffix in
let intervals_option = Region.to_samtools_specification region in
let output_file_prefix = result_file "-out" in
let output_file = output_file_prefix ^ ".MuSE.txt" in
let run_path = Filename.dirname output_file in
let fasta = Reference_genome.fasta reference in
let fasta_dot_fai = Samtools.faidx ~run_with fasta in
let sorted_normal =
Samtools.sort_bam_if_necessary ~run_with ~by:`Coordinate normal in
let sorted_tumor =
Samtools.sort_bam_if_necessary ~run_with ~by:`Coordinate tumor in
let run_muse_call =
let name = sprintf "muse-call-%s" (Filename.basename output_file) in
let make =
Machine.run_program run_with ~name Program.(
Machine.Tool.(init muse_tool)
&& shf "mkdir -p %s" run_path
&& shf "$muse_bin call -f %s %s -O %s %s %s"
fasta#product#path
(match intervals_option with
| Some o -> sprintf "-r %s" o
| None -> "")
output_file_prefix
sorted_tumor#product#path
sorted_normal#product#path
)
in
workflow_node ~name ~make
(vcf_file output_file
~reference_build:normal#product#reference_build
~host:Machine.(as_host run_with))
~tags:[Target_tags.variant_caller; "muse"]
~edges:[
depends_on Machine.Tool.(ensure muse_tool);
depends_on sorted_normal;
depends_on sorted_tumor;
depends_on fasta;
depends_on fasta_dot_fai;
depends_on (Samtools.index_to_bai ~run_with sorted_normal);
depends_on (Samtools.index_to_bai ~run_with sorted_tumor);
on_failure_activate (Remove.file ~run_with output_file);
]
in
run_muse_call
in
let muse_sump call_file =
let vcf_output = result_prefix ^ ".vcf" in
let dbsnp = Reference_genome.dbsnp_exn reference in
let bgzipped_dbsnp =
Samtools.bgzip ~run_with dbsnp (dbsnp#product#path ^ ".bgz") in
let name = sprintf "muse-sump-%s" (Filename.basename vcf_output) in
let make =
Machine.run_program run_with ~name Program.(
Machine.Tool.(init muse_tool)
&& shf "$muse_bin sump -I %s %s -O %s -D %s"
call_file#product#path
Configuration.(match configuration.input_type with
| `WGS -> "-G" | `WES -> "-E")
vcf_output
bgzipped_dbsnp#product#path
)
in
workflow_node ~name ~make
(vcf_file vcf_output
~reference_build:normal#product#reference_build
~host:Machine.(as_host run_with))
~tags:[Target_tags.variant_caller; "muse"]
~edges:(more_edges @ [
depends_on Machine.Tool.(ensure muse_tool);
depends_on call_file;
depends_on bgzipped_dbsnp;
depends_on
(Samtools.tabix ~run_with ~tabular_format:`Vcf bgzipped_dbsnp);
on_failure_activate (Remove.file ~run_with vcf_output);
])
in
begin match how with
| `Region region ->
muse_call_on_region region |> muse_sump
| `Map_reduce ->
let call_files =
List.map (Reference_genome.major_contigs reference) ~f:muse_call_on_region
in
let concatenated =
Workflow_utilities.Cat.concat ~run_with call_files
~result_path:(result_prefix ^ "-concat.txt")
in
muse_sump concatenated
end
end