sig
module type Semantics = Biokepi_pipeline_edsl.Semantics.Bioinformatics_base
module Compile :
sig
module To_display = Biokepi_pipeline_edsl.To_display
module To_workflow = Biokepi_pipeline_edsl.To_workflow
module To_json :
sig
type 'a repr = var_count:int -> Yojson.Basic.json
val lambda : ('a repr -> 'b repr) -> ('a -> 'b) repr
val apply : ('a -> 'b) repr -> 'a repr -> 'b repr
type 'a observation = Yojson.Basic.json
val observe : (unit -> 'a repr) -> 'a observation
val list : 'a repr list -> 'a list repr
val list_map : 'a list repr -> f:('a -> 'b) repr -> 'b list repr
val pair : 'a repr -> 'b repr -> ('a * 'b) repr
val pair_first : ('a * 'b) repr -> 'a repr
val pair_second : ('a * 'b) repr -> 'b repr
val to_unit : 'a repr -> unit repr
val input_url : string -> [ `Raw_file ] repr
val save : name:string -> 'a repr -> [ `Saved of 'a ] repr
val fastq :
sample_name:string ->
?fragment_id:string ->
r1:[ `Raw_file ] repr ->
?r2:[ `Raw_file ] repr -> unit -> [ `Fastq ] repr
val fastq_gz :
sample_name:string ->
?fragment_id:string ->
r1:[ `Raw_file ] repr ->
?r2:[ `Raw_file ] repr -> unit -> [ `Gz of [ `Fastq ] ] repr
val bam :
sample_name:string ->
?sorting:[ `Coordinate | `Read_name ] ->
reference_build:string -> [ `Raw_file ] repr -> [ `Bam ] repr
val bed : [ `Raw_file ] repr -> [ `Bed ] repr
val mhc_alleles :
[ `File of [ `Raw_file ] repr | `Names of string list ] ->
[ `MHC_alleles ] repr
val index_bam : [ `Bam ] repr -> [ `Bai ] repr
val kallisto :
reference_build:string ->
?bootstrap_samples:int ->
[ `Fastq ] repr -> [ `Kallisto_result ] repr
val cufflinks :
?reference_build:string ->
[ `Bam ] repr -> [ `Cufflinks_result ] repr
val gunzip : [ `Gz of 'a ] repr -> 'a repr
val gunzip_concat : [ `Gz of 'a ] list repr -> 'a repr
val concat : 'a list repr -> 'a repr
val merge_bams :
?delete_input_on_success:bool ->
?attach_rg_tag:bool ->
?uncompressed_bam_output:bool ->
?compress_level_one:bool ->
?combine_rg_headers:bool ->
?combine_pg_headers:bool -> [ `Bam ] list repr -> [ `Bam ] repr
val bam_to_fastq :
?fragment_id:string ->
[ `PE | `SE ] -> [ `Bam ] repr -> [ `Fastq ] repr
val bwa_aln :
?configuration:Biokepi_bfx_tools.Bwa.Configuration.Aln.t ->
reference_build:Biokepi_run_environment.Reference_genome.name ->
[ `Fastq ] repr -> [ `Bam ] repr
val bwa_mem :
?configuration:Biokepi_bfx_tools.Bwa.Configuration.Mem.t ->
reference_build:Biokepi_run_environment.Reference_genome.name ->
[ `Fastq ] repr -> [ `Bam ] repr
val bwa_mem_opt :
?configuration:Biokepi_bfx_tools.Bwa.Configuration.Mem.t ->
reference_build:Biokepi_run_environment.Reference_genome.name ->
[ `Bam of [ `Bam ] repr * [ `PE | `SE ]
| `Fastq of [ `Fastq ] repr
| `Fastq_gz of [ `Gz of [ `Fastq ] ] repr ] -> [ `Bam ] repr
val star :
?configuration:Biokepi_bfx_tools.Star.Configuration.Align.t ->
reference_build:Biokepi_run_environment.Reference_genome.name ->
[ `Fastq ] repr -> [ `Bam ] repr
val hisat :
?configuration:Biokepi_bfx_tools.Hisat.Configuration.t ->
reference_build:Biokepi_run_environment.Reference_genome.name ->
[ `Fastq ] repr -> [ `Bam ] repr
val mosaik :
reference_build:Biokepi_run_environment.Reference_genome.name ->
[ `Fastq ] repr -> [ `Bam ] repr
val stringtie :
?configuration:Biokepi_bfx_tools.Stringtie.Configuration.t ->
[ `Bam ] repr -> [ `Gtf ] repr
val gatk_indel_realigner :
?configuration:Biokepi_bfx_tools.Gatk.Configuration.indel_realigner ->
[ `Bam ] repr -> [ `Bam ] repr
val gatk_indel_realigner_joint :
?configuration:Biokepi_bfx_tools.Gatk.Configuration.indel_realigner ->
([ `Bam ] * [ `Bam ]) repr -> ([ `Bam ] * [ `Bam ]) repr
val picard_mark_duplicates :
?configuration:Biokepi_bfx_tools.Picard.Mark_duplicates_settings.t ->
[ `Bam ] repr -> [ `Bam ] repr
val picard_reorder_sam :
?mem_param:string ->
?reference_build:string -> [ `Bam ] repr -> [ `Bam ] repr
val picard_clean_bam : [ `Bam ] repr -> [ `Bam ] repr
val gatk_bqsr :
?configuration:Biokepi_bfx_tools.Gatk.Configuration.bqsr ->
[ `Bam ] repr -> [ `Bam ] repr
val seq2hla : [ `Fastq ] repr -> [ `Seq2hla_result ] repr
val optitype :
[ `DNA | `RNA ] -> [ `Fastq ] repr -> [ `Optitype_result ] repr
val hlarp :
[ `Optitype of [ `Optitype_result ] repr
| `Seq2hla of [ `Seq2hla_result ] repr ] -> [ `MHC_alleles ] repr
val filter_to_region :
[ `Vcf ] repr -> [ `Bed ] repr -> [ `Vcf ] repr
val bam_left_align :
reference_build:string -> [ `Bam ] repr -> [ `Bam ] repr
val sambamba_filter :
filter:Biokepi_bfx_tools.Sambamba.Filter.t ->
[ `Bam ] repr -> [ `Bam ] repr
val gatk_haplotype_caller : [ `Bam ] repr -> [ `Vcf ] repr
val mutect :
?configuration:Biokepi_bfx_tools.Mutect.Configuration.t ->
normal:[ `Bam ] repr ->
tumor:[ `Bam ] repr -> unit -> [ `Vcf ] repr
val mutect2 :
?configuration:Biokepi_bfx_tools.Gatk.Configuration.Mutect2.t ->
normal:[ `Bam ] repr ->
tumor:[ `Bam ] repr -> unit -> [ `Vcf ] repr
val somaticsniper :
?configuration:Biokepi_bfx_tools.Somaticsniper.Configuration.t ->
normal:[ `Bam ] repr ->
tumor:[ `Bam ] repr -> unit -> [ `Vcf ] repr
val delly2 :
?configuration:Biokepi_bfx_tools.Delly2.Configuration.t ->
normal:[ `Bam ] repr ->
tumor:[ `Bam ] repr -> unit -> [ `Vcf ] repr
val varscan_somatic :
?adjust_mapq:int ->
normal:[ `Bam ] repr ->
tumor:[ `Bam ] repr -> unit -> [ `Vcf ] repr
val strelka :
?configuration:Biokepi_bfx_tools.Strelka.Configuration.t ->
normal:[ `Bam ] repr ->
tumor:[ `Bam ] repr -> unit -> [ `Vcf ] repr
val virmid :
?configuration:Biokepi_bfx_tools.Virmid.Configuration.t ->
normal:[ `Bam ] repr ->
tumor:[ `Bam ] repr -> unit -> [ `Vcf ] repr
val muse :
?configuration:Biokepi_bfx_tools.Muse.Configuration.t ->
normal:[ `Bam ] repr ->
tumor:[ `Bam ] repr -> unit -> [ `Vcf ] repr
val fastqc : [ `Fastq ] repr -> [ `Fastqc ] repr
val flagstat : [ `Bam ] repr -> [ `Flagstat ] repr
val vcf_annotate_polyphen : [ `Vcf ] repr -> [ `Vcf ] repr
val snpeff : [ `Vcf ] repr -> [ `Vcf ] repr
val isovar :
?configuration:Biokepi_bfx_tools.Isovar.Configuration.t ->
[ `Vcf ] repr -> [ `Bam ] repr -> [ `Isovar ] repr
val topiary :
?configuration:Biokepi_bfx_tools.Topiary.Configuration.t ->
[ `Vcf ] repr list ->
Biokepi_run_environment.Hla_utilities.predictor_type ->
[ `MHC_alleles ] repr -> [ `Topiary ] repr
val vaxrank :
?configuration:Biokepi_bfx_tools.Vaxrank.Configuration.t ->
[ `Vcf ] repr list ->
[ `Bam ] repr ->
Biokepi_run_environment.Hla_utilities.predictor_type ->
[ `MHC_alleles ] repr -> [ `Vaxrank ] repr
val seqtk_shift_phred_scores : [ `Fastq ] repr -> [ `Fastq ] repr
end
module To_dot :
sig
type 'a repr = var_count:int -> Biokepi_pipeline_edsl.To_dot.Tree.t
val lambda : ('a repr -> 'b repr) -> ('a -> 'b) repr
val apply : ('a -> 'b) repr -> 'a repr -> 'b repr
type 'a observation =
parameters:Biokepi_pipeline_edsl.To_dot.parameters ->
SmartPrint.t
val observe : (unit -> 'a repr) -> 'a observation
val list : 'a repr list -> 'a list repr
val list_map : 'a list repr -> f:('a -> 'b) repr -> 'b list repr
val pair : 'a repr -> 'b repr -> ('a * 'b) repr
val pair_first : ('a * 'b) repr -> 'a repr
val pair_second : ('a * 'b) repr -> 'b repr
val to_unit : 'a repr -> unit repr
val input_url : string -> [ `Raw_file ] repr
val save : name:string -> 'a repr -> [ `Saved of 'a ] repr
val fastq :
sample_name:string ->
?fragment_id:string ->
r1:[ `Raw_file ] repr ->
?r2:[ `Raw_file ] repr -> unit -> [ `Fastq ] repr
val fastq_gz :
sample_name:string ->
?fragment_id:string ->
r1:[ `Raw_file ] repr ->
?r2:[ `Raw_file ] repr -> unit -> [ `Gz of [ `Fastq ] ] repr
val bam :
sample_name:string ->
?sorting:[ `Coordinate | `Read_name ] ->
reference_build:string -> [ `Raw_file ] repr -> [ `Bam ] repr
val bed : [ `Raw_file ] repr -> [ `Bed ] repr
val mhc_alleles :
[ `File of [ `Raw_file ] repr | `Names of string list ] ->
[ `MHC_alleles ] repr
val index_bam : [ `Bam ] repr -> [ `Bai ] repr
val kallisto :
reference_build:string ->
?bootstrap_samples:int ->
[ `Fastq ] repr -> [ `Kallisto_result ] repr
val cufflinks :
?reference_build:string ->
[ `Bam ] repr -> [ `Cufflinks_result ] repr
val gunzip : [ `Gz of 'a ] repr -> 'a repr
val gunzip_concat : [ `Gz of 'a ] list repr -> 'a repr
val concat : 'a list repr -> 'a repr
val merge_bams :
?delete_input_on_success:bool ->
?attach_rg_tag:bool ->
?uncompressed_bam_output:bool ->
?compress_level_one:bool ->
?combine_rg_headers:bool ->
?combine_pg_headers:bool -> [ `Bam ] list repr -> [ `Bam ] repr
val bam_to_fastq :
?fragment_id:string ->
[ `PE | `SE ] -> [ `Bam ] repr -> [ `Fastq ] repr
val bwa_aln :
?configuration:Biokepi_bfx_tools.Bwa.Configuration.Aln.t ->
reference_build:Biokepi_run_environment.Reference_genome.name ->
[ `Fastq ] repr -> [ `Bam ] repr
val bwa_mem :
?configuration:Biokepi_bfx_tools.Bwa.Configuration.Mem.t ->
reference_build:Biokepi_run_environment.Reference_genome.name ->
[ `Fastq ] repr -> [ `Bam ] repr
val bwa_mem_opt :
?configuration:Biokepi_bfx_tools.Bwa.Configuration.Mem.t ->
reference_build:Biokepi_run_environment.Reference_genome.name ->
[ `Bam of [ `Bam ] repr * [ `PE | `SE ]
| `Fastq of [ `Fastq ] repr
| `Fastq_gz of [ `Gz of [ `Fastq ] ] repr ] -> [ `Bam ] repr
val star :
?configuration:Biokepi_bfx_tools.Star.Configuration.Align.t ->
reference_build:Biokepi_run_environment.Reference_genome.name ->
[ `Fastq ] repr -> [ `Bam ] repr
val hisat :
?configuration:Biokepi_bfx_tools.Hisat.Configuration.t ->
reference_build:Biokepi_run_environment.Reference_genome.name ->
[ `Fastq ] repr -> [ `Bam ] repr
val mosaik :
reference_build:Biokepi_run_environment.Reference_genome.name ->
[ `Fastq ] repr -> [ `Bam ] repr
val stringtie :
?configuration:Biokepi_bfx_tools.Stringtie.Configuration.t ->
[ `Bam ] repr -> [ `Gtf ] repr
val gatk_indel_realigner :
?configuration:Biokepi_bfx_tools.Gatk.Configuration.indel_realigner ->
[ `Bam ] repr -> [ `Bam ] repr
val gatk_indel_realigner_joint :
?configuration:Biokepi_bfx_tools.Gatk.Configuration.indel_realigner ->
([ `Bam ] * [ `Bam ]) repr -> ([ `Bam ] * [ `Bam ]) repr
val picard_mark_duplicates :
?configuration:Biokepi_bfx_tools.Picard.Mark_duplicates_settings.t ->
[ `Bam ] repr -> [ `Bam ] repr
val picard_reorder_sam :
?mem_param:string ->
?reference_build:string -> [ `Bam ] repr -> [ `Bam ] repr
val picard_clean_bam : [ `Bam ] repr -> [ `Bam ] repr
val gatk_bqsr :
?configuration:Biokepi_bfx_tools.Gatk.Configuration.bqsr ->
[ `Bam ] repr -> [ `Bam ] repr
val seq2hla : [ `Fastq ] repr -> [ `Seq2hla_result ] repr
val optitype :
[ `DNA | `RNA ] -> [ `Fastq ] repr -> [ `Optitype_result ] repr
val hlarp :
[ `Optitype of [ `Optitype_result ] repr
| `Seq2hla of [ `Seq2hla_result ] repr ] -> [ `MHC_alleles ] repr
val filter_to_region :
[ `Vcf ] repr -> [ `Bed ] repr -> [ `Vcf ] repr
val bam_left_align :
reference_build:string -> [ `Bam ] repr -> [ `Bam ] repr
val sambamba_filter :
filter:Biokepi_bfx_tools.Sambamba.Filter.t ->
[ `Bam ] repr -> [ `Bam ] repr
val gatk_haplotype_caller : [ `Bam ] repr -> [ `Vcf ] repr
val mutect :
?configuration:Biokepi_bfx_tools.Mutect.Configuration.t ->
normal:[ `Bam ] repr ->
tumor:[ `Bam ] repr -> unit -> [ `Vcf ] repr
val mutect2 :
?configuration:Biokepi_bfx_tools.Gatk.Configuration.Mutect2.t ->
normal:[ `Bam ] repr ->
tumor:[ `Bam ] repr -> unit -> [ `Vcf ] repr
val somaticsniper :
?configuration:Biokepi_bfx_tools.Somaticsniper.Configuration.t ->
normal:[ `Bam ] repr ->
tumor:[ `Bam ] repr -> unit -> [ `Vcf ] repr
val delly2 :
?configuration:Biokepi_bfx_tools.Delly2.Configuration.t ->
normal:[ `Bam ] repr ->
tumor:[ `Bam ] repr -> unit -> [ `Vcf ] repr
val varscan_somatic :
?adjust_mapq:int ->
normal:[ `Bam ] repr ->
tumor:[ `Bam ] repr -> unit -> [ `Vcf ] repr
val strelka :
?configuration:Biokepi_bfx_tools.Strelka.Configuration.t ->
normal:[ `Bam ] repr ->
tumor:[ `Bam ] repr -> unit -> [ `Vcf ] repr
val virmid :
?configuration:Biokepi_bfx_tools.Virmid.Configuration.t ->
normal:[ `Bam ] repr ->
tumor:[ `Bam ] repr -> unit -> [ `Vcf ] repr
val muse :
?configuration:Biokepi_bfx_tools.Muse.Configuration.t ->
normal:[ `Bam ] repr ->
tumor:[ `Bam ] repr -> unit -> [ `Vcf ] repr
val fastqc : [ `Fastq ] repr -> [ `Fastqc ] repr
val flagstat : [ `Bam ] repr -> [ `Flagstat ] repr
val vcf_annotate_polyphen : [ `Vcf ] repr -> [ `Vcf ] repr
val snpeff : [ `Vcf ] repr -> [ `Vcf ] repr
val isovar :
?configuration:Biokepi_bfx_tools.Isovar.Configuration.t ->
[ `Vcf ] repr -> [ `Bam ] repr -> [ `Isovar ] repr
val topiary :
?configuration:Biokepi_bfx_tools.Topiary.Configuration.t ->
[ `Vcf ] repr list ->
Biokepi_run_environment.Hla_utilities.predictor_type ->
[ `MHC_alleles ] repr -> [ `Topiary ] repr
val vaxrank :
?configuration:Biokepi_bfx_tools.Vaxrank.Configuration.t ->
[ `Vcf ] repr list ->
[ `Bam ] repr ->
Biokepi_run_environment.Hla_utilities.predictor_type ->
[ `MHC_alleles ] repr -> [ `Vaxrank ] repr
val seqtk_shift_phred_scores : [ `Fastq ] repr -> [ `Fastq ] repr
type parameters =
Biokepi_pipeline_edsl.To_dot.parameters = {
color_input :
name:string ->
attributes:(string * string) list -> string option;
}
val default_parameters : Biokepi.EDSL.Compile.??.parameters
end
end
module Transform :
sig
module Apply_functions =
Biokepi_pipeline_edsl.Transform_applications.Apply
end
module Library = Biokepi_pipeline_edsl.Pipeline_library
end