let gunzip: type a. [ `Gz of a ] t -> a t = fun gz ->
let inside = get_gz gz in
begin match inside with
| Fastq f ->
let make_result_path read =
let base = Filename.basename read in
Config.work_dir //
(match base with
| fastqgz when Filename.check_suffix base ".fastq.gz" ->
Filename.chop_suffix base ".gz"
| fqz when Filename.check_suffix base ".fqz" ->
Filename.chop_suffix base ".fqz" ^ ".fastq"
| other ->
ksprintf failwith "To_workflow.gunzip: cannot recognize Gz-Fastq extension: %S" other)
in
let gunzip read =
let result_path = make_result_path read#product#path in
Workflow_utilities.Gunzip.concat
~run_with [read] ~result_path in
let fastq_r1 = gunzip f#product#r1 in
let fastq_r2 = Option.map f#product#r2 ~f:gunzip in
Fastq (
KEDSL.fastq_node_of_single_file_nodes ~host
~name:f#product#sample_name
?fragment_id:f#product#fragment_id
fastq_r1 fastq_r2
)
| other ->
ksprintf failwith "To_workflow.gunzip: non-FASTQ input not implemented"
end