module Pipeline:sig
..end
module File:sig
..end
typejson =
Yojson.Basic.json
type
fastq_gz =
| |
Fastq_gz |
type
fastq =
| |
Fastq |
type
fastq_sample =
| |
Fastq_sample |
typebam =
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 |
type
optitype_hla_types =
| |
Optitype_hla_types |
type
somatic = {
|
normal : |
|
tumor : |
typegermline =
bam
type
fastq_sample_info = {
|
sample_name : |
|
fragment_id : |
module Variant_caller:sig
..end
typemetadata_spec =
[ `Add_tags of string list | `Add_tags_rec of string list ]
type '_
t =
| |
Fastq_gz : |
| |
Fastq : |
| |
Bam_sample : |
| |
Bam_to_fastq : |
| |
Paired_end_sample : |
| |
Single_end_sample : |
| |
Gunzip_concat : |
| |
Concat_text : |
| |
Star : |
| |
Hisat : |
| |
Stringtie : |
| |
Bwa : |
| |
Bwa_mem : |
| |
Mosaik : |
| |
Gatk_indel_realigner : |
| |
Picard_mark_duplicates : |
| |
Gatk_bqsr : |
| |
Bam_pair : |
| |
Somatic_variant_caller : |
| |
Germline_variant_caller : |
| |
Seq2HLA : |
| |
Optitype : |
| |
With_metadata : |
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