Module type Biokepi.EDSL.Semantics

module type Semantics = Biokepi_pipeline_edsl.Semantics.Bioinformatics_base

The definition of the Embedded DSL

include Biokepi_pipeline_edsl.Semantics.Lambda_with_list_operations

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

This is used to opacify the type of the expression.

val input_url : string -> [ `Raw_file ] repr

Decrlare an URL as a input to a a pipeline.

If the URL has the scheme "file://" or no scheme it will be treated as a “local file” (i.e. local to the Biokepi.Machine.t).
If the URL has the schemes "http://" or "https://" the file will be downloaded into the work-directory.
If the URL has the scheme "gs://" the file will be fetched thanks to "gsutil" (Google Cloud's storage buckets management tool).

For both "http(s)://" and "gs://" schemes one can override the local filename, by adding a "filename" argument to the query part of the URL. E.g. "https://data.example.com/my-sample.bam?filename=sample-from-example.bam".

val save : name:string -> 'a repr -> [ `Saved of 'a ] repr

Tag a product of the EDSL as “interesting to be saved” (the meaning is implementation dependent; when compiling to a Ketrew workflow this means copying the file(s) to another directory.

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

Input a file containing HLA allelles for Topiary

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

Optimized version of bwa-mem.

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

FreeBayes' bamleftalign utility, which left-normalizes indels. That is, indels which could be aligned multiple ways (e.g. AAA_G_GAA is the same as AAAG_G_AA) are moved to the left, as in the first example. This is so that they can be treated uniformly in post-processing.

val sambamba_filter : filter:Biokepi_bfx_tools.Sambamba.Filter.t -> [ `Bam ] repr -> [ `Bam ] repr

Sambamba's view filter tool, used to filter down a BAM to one with reads matching some predicate (filter language at https://github.com/lomereiter/sambamba/wiki/%5Bsambamba-view%5D-Filter-expression-syntax).

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

Run delly2 on a tumor/normal sample.

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

Call the FASTQC tool (the result is an output directory custom to the tool).

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