struct
open Biokepi_run_environment
open Common
let run ~(run_with:Machine.t) ~fastq ~output_folder =
let open KEDSL in
let open Ketrew_pure.Target.Volume in
let fastqc = Machine.get_tool run_with Machine.Tool.Default.fastqc in
let paths =
let r1_path, r2_path_opt = fastq#product#paths in
match r2_path_opt with
| Some r2_path -> [r1_path; r2_path]
| None -> [r1_path]
in
let get_file_name path =
let parts = String.split path ~on:(`Character '/') |> List.rev in
match parts with
| [] -> failwith "Couldn't guess the fastq filename from the path."
| hd :: tl -> hd
in
let output_files =
paths
|> List.map ~f:get_file_name
|> List.map ~f:(fun p -> Re.replace_string (Re_posix.compile_pat ".fastq$") "_fastqc.html" p)
|> List.map ~f:(fun p -> output_folder // p)
in
let paths_str = String.concat paths ~sep:" " in
let cmd = sprintf "$FASTQC_BIN --extract -o %s %s" output_folder paths_str in
let name = sprintf "FastQC_%s" output_folder in
let make =
Machine.run_big_program run_with ~name
~self_ids:["fastqc"]
Program.(Machine.Tool.(init fastqc) && shf "mkdir -p %s" output_folder && sh cmd)
in
workflow_node ~name ~make
(list_of_files output_files ~host:(Machine.as_host run_with))
~edges: [
on_failure_activate (Workflow_utilities.Remove.directory ~run_with output_folder);
depends_on (Machine.Tool.ensure fastqc);
depends_on fastq;
]
end