Module Biokepi_pipeline_edsl.Pipeline (.ml)

module Pipeline: sig .. end

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