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Module Biokepi.Pipeline (.ml)

module Pipeline: Biokepi_pipeline_edsl.Pipeline
Earlier implementation of the Embedded DSL (kept for backwards compatibility).

Biokepi.Pipeline.t is a GADT describing high-level workflows.

One defines pipelines using the Biokepi.Pipeline.Construct module and compiles them to JSON or to Ketrew workflows.

See "src/pipeline_edsl/common_pipelines.ml" and "src/app/main.ml" for examples.

module File: sig .. end
type json = Yojson.Basic.json 
type fastq_gz =
| Fastq_gz 
type fastq =
| Fastq 
type fastq_sample =
| Fastq_sample 
type bam = Biokepi_run_environment.Common.KEDSL.bam_file
       Biokepi_run_environment.Common.KEDSL.workflow_node 
type bam_pair =
| Bam_pair 
type vcf =
| Vcf 
type gtf =
| Gtf 
type seq2hla_hla_types =
| Seq2HLA_hla_types
Seq2HLA & Optitype have unique return file formats
type optitype_hla_types =
| Optitype_hla_types 
type somatic = {
   normal : bam;
   tumor : bam;
} 
type germline = bam 
type fastq_sample_info = {
   sample_name : string;
   fragment_id : string;
} 
module Variant_caller: sig .. end
type metadata_spec = [ `Add_tags of string list | `Add_tags_rec of string list ] 
type '_ t =
| Fastq_gz : File.t -> fastq_gz t
| Fastq : File.t -> fastq t
| Bam_sample : string * bam -> bam t
| Bam_to_fastq : [ `Paired | `Single ]
* bam t -> fastq_sample t
| Paired_end_sample : fastq_sample_info
* fastq t
* fastq t -> fastq_sample t
| Single_end_sample : fastq_sample_info
* fastq t -> fastq_sample t
| Gunzip_concat : fastq_gz t list -> fastq t
| Concat_text : fastq t list -> fastq t
| Star : Biokepi_bfx_tools.Star.Configuration.Align.t
* fastq_sample
t -> bam t
| Hisat : Biokepi_bfx_tools.Hisat.Configuration.t
* fastq_sample
t -> bam t
| Stringtie : Biokepi_bfx_tools.Stringtie.Configuration.t
* bam t -> gtf t
| Bwa : Biokepi_bfx_tools.Bwa.Configuration.Aln.t
* fastq_sample
t -> bam t
| Bwa_mem : Biokepi_bfx_tools.Bwa.Configuration.Mem.t
* fastq_sample
t -> bam t
| Mosaik : fastq_sample t -> bam t
| Gatk_indel_realigner : Biokepi_bfx_tools.Gatk.Configuration.indel_realigner
* bam t -> bam t
| Picard_mark_duplicates : Biokepi_bfx_tools.Picard.Mark_duplicates_settings.t
* bam t -> bam t
| Gatk_bqsr : (Biokepi_bfx_tools.Gatk.Configuration.bqsr *
bam t) -> bam t
| Bam_pair : bam t
* bam t -> bam_pair t
| Somatic_variant_caller : somatic
Variant_caller.t
* bam_pair t -> vcf t
| Germline_variant_caller : germline
Variant_caller.t
* bam t -> vcf t
| Seq2HLA : fastq_sample t -> seq2hla_hla_types
t
| Optitype : ([ `DNA | `RNA ] *
fastq_sample t) -> optitype_hla_types
t
| With_metadata : metadata_spec
* 'a t -> 'a t		 
module Construct: sig .. end
val to_file_prefix : 'a.
         ?read:[ `R1 of string | `R2 of string ] ->
         'a t -> string
val to_json : 'a.
         'a t -> json
module Compiler: sig .. end