Functor Biokepi_pipeline_edsl.Pipeline_library.Make (.ml)

module Make: functor (Bfx : Semantics.Bioinformatics_base) -> sig .. end

Parameters:

Bfx : Semantics.Bioinformatics_base

val fastq_of_files : sample_name:string ->
       ?fragment_id:string -> r1:string -> ?r2:string -> unit -> [ `Fastq ] Bfx.repr

This functions guesses whether to use fastq or fastq_gz given the file name extension. If r1 and r2 dot match, it fails with an exception.

val bam_of_input_exn : Biokepi_pipeline_edsl.Pipeline_library.Input.t -> [ `Bam ] Bfx.repr

Transform a value of type Input.t into a list of BAMs.

val fastq_of_input : Biokepi_pipeline_edsl.Pipeline_library.Input.t -> [ `Fastq ] list Bfx.repr

Transform a value of type Input.t into a pipeline returning FASTQ data, providing the necessary intermediary steps.

val bwa_mem_opt_inputs_exn : Biokepi_pipeline_edsl.Pipeline_library.Input.t ->
       [> `Bam of
            [ `Bam ] Bfx.repr * Biokepi_pipeline_edsl.Pipeline_library.Input.how
        | `Fastq of [ `Fastq ] Bfx.repr
        | `Fastq_gz of [ `Gz of [ `Fastq ] ] Bfx.repr ]
       list