let fastqs ?(paired_end=true) ~host dir = let open Pvem_lwt_unix.Deferred_result in (* We only want to select fastq.gzs in the directory: *) let fastq_re = Re.compile (Re_posix.re {re|.*\.fastq\.gz|re}) in let fastq_p = Re.execp fastq_re in let r1_to_r2 s = let r1_re = Re.compile (Re_posix.re "_R1_") in Re.replace_string r1_re ~by:"_R2_" s in (* If we're expecting paired_end reads, make sure we have a R2 in the directory for each R1 fragment. Returns the list of R1 fragments. *) let ensure_matching_r2s files = if paired_end then (List.fold ~init:(return []) files ~f:(fun acc r1 -> acc >>= fun r1s -> match String.index_of_string r1 ~sub:"_R1_" with | None -> acc | Some _ -> if List.mem (r1_to_r2 r1) ~set:files then return (r1 :: r1s) else fail (`R2_expected_for_r1 r1))) else return files in let as_fragments read1s_filenames = List.mapi read1s_filenames ~f:(fun i r1 -> if paired_end then let r2 = dir // (r1_to_r2 r1) in let r1 = dir // r1 in let fragment_id = sprintf "fragment-%d" i in pe ~fragment_id r1 r2 else let r1 = dir // r1 in let fragment_id = sprintf "fragment-%d" i in se ~fragment_id r1) |> return in let cmd = (sprintf "ls '%s' | sort" dir) in Ketrew.Host_io.(get_shell_command_output (create ()) ~host:host cmd) >>= fun (out, err) -> String.split ~on:(`Character '\n') out |> List.filter ~f:fastq_p |> return >>= ensure_matching_r2s >>= ensure_one_flowcell_max >>= as_fragments