struct
open Biokepi_run_environment
open Common
(**
Run OptiType in `RNA or `DNA mode.
Please provide a fresh |
let hla_type ~work_dir ~run_with ~fastq ~run_name nt =
let tool = Machine.get_tool run_with Machine.Tool.Default.optitype in
let r1_path, r2_path_opt = fastq#product#paths in
let name = sprintf "optitype-%s" run_name in
let make =
Machine.run_big_program run_with ~name
~self_ids:["optitype"]
KEDSL.Program.(
Machine.Tool.init tool
&& exec ["mkdir"; "-p"; work_dir]
&& exec ["cd"; work_dir]
&& sh "cp -r ${OPTITYPE_DATA}/data ." (* HLA reference data *)
&& (* config example *)
sh "cp -r ${OPTITYPE_DATA}/config.ini.example config.ini"
&& (* adjust config razers3 path *)
sh "sed -i.bak \"s|\\/path\\/to\\/razers3|$(which razers3)|g\" config.ini"
&&
shf "OptiTypePipeline --verbose --input %s %s %s -o %s "
(Filename.quote r1_path)
(Option.value_map ~default:"" r2_path_opt ~f:Filename.quote)
(match nt with | `DNA -> "--dna" | `RNA -> "--rna")
run_name)
in
let product =
let host = Machine.as_host run_with in
let vol =
let open Ketrew_pure.Target.Volume in
create (dir run_name []) ~host
~root:(Ketrew_pure.Path.absolute_directory_exn work_dir)
in
object
method is_done = Some (`Volume_exists vol)
method path = work_dir
end
in
KEDSL.workflow_node product ~name ~make
~edges:(
[
KEDSL.depends_on (Machine.Tool.ensure tool);
KEDSL.depends_on fastq;
KEDSL.on_failure_activate
(Workflow_utilities.Remove.directory ~run_with work_dir);
]
)
end