Functor Biokepi_pipeline_edsl.To_json.Make_serializer (.ml)

module Make_serializer: 
functor (How : sig

type t 


val input_value : string ->
       (string * string) list -> var_count:int -> t
val function_call : string ->
       (string * t) list ->
       t
val string : string -> t
end) -> sig .. end

val input_url : string -> var_count:int -> How.t

val save : name:string -> (var_count:'a -> How.t) -> var_count:'a -> How.t

val fastq_or_gz : string ->
       sample_name:string ->
       ?fragment_id:string ->
       r1:(var_count:'a -> How.t) ->
       ?r2:(var_count:'a -> How.t) -> unit -> var_count:'a -> How.t

val fastq : sample_name:string ->
       ?fragment_id:string ->
       r1:(var_count:'a -> How.t) ->
       ?r2:(var_count:'a -> How.t) -> unit -> var_count:'a -> How.t

val fastq_gz : sample_name:string ->
       ?fragment_id:string ->
       r1:(var_count:'a -> How.t) ->
       ?r2:(var_count:'a -> How.t) -> unit -> var_count:'a -> How.t

val bam : sample_name:string ->
       ?sorting:[< `Coordinate | `Read_name ] ->
       reference_build:string -> (var_count:'a -> How.t) -> var_count:'a -> How.t

val bed : (var_count:'a -> How.t) -> var_count:'a -> How.t

val mhc_alleles : [< `File of var_count:int -> How.t | `Names of string list ] ->
       var_count:int -> How.t

val pair : (var_count:int -> How.t) ->
       (var_count:int -> How.t) -> var_count:int -> How.t

val pair_first : (var_count:int -> How.t) -> var_count:int -> How.t

val pair_second : (var_count:int -> How.t) -> var_count:int -> How.t

val aligner : string ->
       string ->
       reference_build:string -> (var_count:int -> How.t) -> var_count:int -> How.t

val one_to_one : string -> string -> (var_count:int -> How.t) -> var_count:int -> How.t

val bwa_aln : ?configuration:Tools.Bwa.Configuration.Aln.t ->
       reference_build:string -> (var_count:int -> How.t) -> var_count:int -> How.t

val bwa_mem : ?configuration:Tools.Bwa.Configuration.Mem.t ->
       reference_build:string -> (var_count:int -> How.t) -> var_count:int -> How.t

val bwa_mem_opt : ?configuration:Tools.Bwa.Configuration.Mem.t ->
       reference_build:string ->
       [< `Bam of (var_count:int -> How.t) * 'a
        | `Fastq of var_count:int -> How.t
        | `Fastq_gz of var_count:int -> How.t ] ->
       var_count:int -> How.t

val gunzip : (var_count:int -> How.t) -> var_count:int -> How.t

val gunzip_concat : (var_count:int -> How.t) -> var_count:int -> How.t

val concat : (var_count:int -> How.t) -> var_count:int -> How.t

val merge_bams : ?delete_input_on_success:'a ->
       ?attach_rg_tag:'b ->
       ?uncompressed_bam_output:'c ->
       ?compress_level_one:'d ->
       ?combine_rg_headers:'e ->
       ?combine_pg_headers:'f -> (var_count:int -> How.t) -> var_count:int -> How.t

val star : ?configuration:Tools.Star.Configuration.Align.t ->
       reference_build:string -> (var_count:int -> How.t) -> var_count:int -> How.t

val hisat : ?configuration:Tools.Hisat.Configuration.t ->
       reference_build:string -> (var_count:int -> How.t) -> var_count:int -> How.t

val mosaik : reference_build:string -> (var_count:int -> How.t) -> var_count:int -> How.t

val stringtie : ?configuration:Tools.Stringtie.Configuration.t ->
       (var_count:int -> How.t) -> var_count:int -> How.t

val bam_left_align : reference_build:string -> (var_count:int -> How.t) -> var_count:int -> How.t

val sambamba_filter : filter:[< `String of string ] ->
       (var_count:int -> How.t) -> var_count:int -> How.t

val indel_real_config : Tools.Gatk.Configuration.Indel_realigner.t *
       Tools.Gatk.Configuration.Realigner_target_creator.t -> string

val gatk_indel_realigner : ?configuration:Tools.Gatk.Configuration.Indel_realigner.t *
                      Tools.Gatk.Configuration.Realigner_target_creator.t ->
       (var_count:int -> How.t) -> var_count:int -> How.t

val gatk_indel_realigner_joint : ?configuration:Tools.Gatk.Configuration.Indel_realigner.t *
                      Tools.Gatk.Configuration.Realigner_target_creator.t ->
       (var_count:int -> How.t) -> var_count:int -> How.t

val picard_mark_duplicates : ?configuration:Tools.Picard.Mark_duplicates_settings.t ->
       (var_count:int -> How.t) -> var_count:int -> How.t

val picard_reorder_sam : ?mem_param:'a ->
       ?reference_build:string -> (var_count:int -> How.t) -> var_count:int -> How.t

val picard_clean_bam : (var_count:int -> How.t) -> var_count:int -> How.t

val gatk_bqsr : ?configuration:Tools.Gatk.Configuration.Bqsr.t *
                      Tools.Gatk.Configuration.Print_reads.t ->
       (var_count:int -> How.t) -> var_count:int -> How.t

val seq2hla : (var_count:int -> How.t) -> var_count:int -> How.t

val hlarp : [< `Optitype of var_count:int -> How.t | `Seq2hla of var_count:int -> How.t ] ->
       var_count:int -> How.t

val filter_to_region : (var_count:int -> How.t) ->
       (var_count:int -> How.t) -> var_count:int -> How.t

val index_bam : (var_count:int -> How.t) -> var_count:int -> How.t

val kallisto : reference_build:string ->
       ?bootstrap_samples:int -> (var_count:int -> How.t) -> var_count:int -> How.t

val cufflinks : ?reference_build:string -> (var_count:int -> How.t) -> var_count:int -> How.t

val fastqc : (var_count:int -> How.t) -> var_count:int -> How.t

val flagstat : (var_count:int -> How.t) -> var_count:int -> How.t

val vcf_annotate_polyphen : (var_count:int -> How.t) -> var_count:int -> How.t

val snpeff : (var_count:int -> How.t) -> var_count:int -> How.t

val isovar : ?configuration:Tools.Isovar.Configuration.t ->
       (var_count:int -> How.t) ->
       (var_count:int -> How.t) -> var_count:int -> How.t

val topiary : ?configuration:Tools.Topiary.Configuration.t ->
       (var_count:int -> How.t) list ->
       [< `NetMHC
        | `NetMHCIIpan
        | `NetMHCcons
        | `NetMHCcons_IEDB
        | `NetMHCpan
        | `NetMHCpan_IEDB
        | `Random
        | `SMM
        | `SMM_IEDB
        | `SMM_PMBEC
        | `SMM_PMBEC_IEDB ] ->
       (var_count:int -> How.t) -> var_count:int -> How.t

val vaxrank : ?configuration:Tools.Vaxrank.Configuration.t ->
       (var_count:int -> How.t) list ->
       (var_count:int -> How.t) ->
       [< `NetMHC
        | `NetMHCIIpan
        | `NetMHCcons
        | `NetMHCcons_IEDB
        | `NetMHCpan
        | `NetMHCpan_IEDB
        | `Random
        | `SMM
        | `SMM_IEDB
        | `SMM_PMBEC
        | `SMM_PMBEC_IEDB ] ->
       (var_count:int -> How.t) -> var_count:int -> How.t

val optitype : [< `DNA | `RNA ] -> (var_count:int -> How.t) -> var_count:int -> How.t

val gatk_haplotype_caller : (var_count:int -> How.t) -> var_count:int -> How.t

val bam_to_fastq : ?fragment_id:string ->
       [< `PE | `SE ] -> (var_count:int -> How.t) -> var_count:int -> How.t

val variant_caller : string ->
       string ->
       normal:(var_count:int -> How.t) ->
       tumor:(var_count:int -> How.t) -> unit -> var_count:int -> How.t

val mutect : ?configuration:Tools.Mutect.Configuration.t ->
       normal:(var_count:int -> How.t) ->
       tumor:(var_count:int -> How.t) -> unit -> var_count:int -> How.t

val mutect2 : ?configuration:Tools.Gatk.Configuration.Mutect2.t ->
       normal:(var_count:int -> How.t) ->
       tumor:(var_count:int -> How.t) -> unit -> var_count:int -> How.t

val delly2 : ?configuration:Tools.Delly2.Configuration.t ->
       normal:(var_count:int -> How.t) ->
       tumor:(var_count:int -> How.t) -> unit -> var_count:int -> How.t

val somaticsniper : ?configuration:Tools.Somaticsniper.Configuration.t ->
       normal:(var_count:int -> How.t) ->
       tumor:(var_count:int -> How.t) -> unit -> var_count:int -> How.t

val strelka : ?configuration:Tools.Strelka.Configuration.t ->
       normal:(var_count:int -> How.t) ->
       tumor:(var_count:int -> How.t) -> unit -> var_count:int -> How.t

val varscan_somatic : ?adjust_mapq:int ->
       normal:(var_count:int -> How.t) ->
       tumor:(var_count:int -> How.t) -> unit -> var_count:int -> How.t

val muse : ?configuration:Tools.Muse.Configuration.t ->
       normal:(var_count:int -> How.t) ->
       tumor:(var_count:int -> How.t) -> unit -> var_count:int -> How.t

val virmid : ?configuration:Tools.Virmid.Configuration.t ->
       normal:(var_count:int -> How.t) ->
       tumor:(var_count:int -> How.t) -> unit -> var_count:int -> How.t

val seqtk_shift_phred_scores : (var_count:int -> How.t) -> var_count:int -> How.t