sig   type input_fastq =       [ `Paired_end of           Biokepi_pipeline_edsl.Pipeline.File.t list *           Biokepi_pipeline_edsl.Pipeline.File.t list       | `Single_end of Biokepi_pipeline_edsl.Pipeline.File.t list ]   val input_fastq :     dataset:string ->     Biokepi_pipeline_edsl.Pipeline.Construct.input_fastq ->     Biokepi_pipeline_edsl.Pipeline.fastq_sample     Biokepi_pipeline_edsl.Pipeline.t   val bam :     dataset:string ->     Biokepi_pipeline_edsl.Pipeline.bam ->     Biokepi_pipeline_edsl.Pipeline.bam Biokepi_pipeline_edsl.Pipeline.t   val bam_to_fastq :     [ `Paired | `Single ] ->     Biokepi_pipeline_edsl.Pipeline.bam Biokepi_pipeline_edsl.Pipeline.t ->     Biokepi_pipeline_edsl.Pipeline.fastq_sample     Biokepi_pipeline_edsl.Pipeline.t   val bwa :     ?configuration:Biokepi_bfx_tools.Bwa.Configuration.Aln.t ->     Biokepi_pipeline_edsl.Pipeline.fastq_sample     Biokepi_pipeline_edsl.Pipeline.t ->     Biokepi_pipeline_edsl.Pipeline.bam Biokepi_pipeline_edsl.Pipeline.t   val bwa_aln :     ?configuration:Biokepi_bfx_tools.Bwa.Configuration.Aln.t ->     Biokepi_pipeline_edsl.Pipeline.fastq_sample     Biokepi_pipeline_edsl.Pipeline.t ->     Biokepi_pipeline_edsl.Pipeline.bam Biokepi_pipeline_edsl.Pipeline.t   val bwa_mem :     ?configuration:Biokepi_bfx_tools.Bwa.Configuration.Mem.t ->     Biokepi_pipeline_edsl.Pipeline.fastq_sample     Biokepi_pipeline_edsl.Pipeline.t ->     Biokepi_pipeline_edsl.Pipeline.bam Biokepi_pipeline_edsl.Pipeline.t   val mosaik :     Biokepi_pipeline_edsl.Pipeline.fastq_sample     Biokepi_pipeline_edsl.Pipeline.t ->     Biokepi_pipeline_edsl.Pipeline.bam Biokepi_pipeline_edsl.Pipeline.t   val star :     ?configuration:Biokepi_bfx_tools.Star.Configuration.Align.t ->     Biokepi_pipeline_edsl.Pipeline.fastq_sample     Biokepi_pipeline_edsl.Pipeline.t ->     Biokepi_pipeline_edsl.Pipeline.bam Biokepi_pipeline_edsl.Pipeline.t   val hisat :     ?configuration:Biokepi_bfx_tools.Hisat.Configuration.t ->     Biokepi_pipeline_edsl.Pipeline.fastq_sample     Biokepi_pipeline_edsl.Pipeline.t ->     Biokepi_pipeline_edsl.Pipeline.bam Biokepi_pipeline_edsl.Pipeline.t   val stringtie :     ?configuration:Biokepi_bfx_tools.Stringtie.Configuration.t ->     Biokepi_pipeline_edsl.Pipeline.bam Biokepi_pipeline_edsl.Pipeline.t ->     Biokepi_pipeline_edsl.Pipeline.gtf Biokepi_pipeline_edsl.Pipeline.t   val gatk_indel_realigner :     ?configuration:Biokepi_bfx_tools.Gatk.Configuration.indel_realigner ->     Biokepi_pipeline_edsl.Pipeline.bam Biokepi_pipeline_edsl.Pipeline.t ->     Biokepi_pipeline_edsl.Pipeline.bam Biokepi_pipeline_edsl.Pipeline.t   val picard_mark_duplicates :     ?settings:Biokepi_bfx_tools.Picard.Mark_duplicates_settings.t ->     Biokepi_pipeline_edsl.Pipeline.bam Biokepi_pipeline_edsl.Pipeline.t ->     Biokepi_pipeline_edsl.Pipeline.bam Biokepi_pipeline_edsl.Pipeline.t   val gatk_bqsr :     ?configuration:Biokepi_bfx_tools.Gatk.Configuration.bqsr ->     Biokepi_pipeline_edsl.Pipeline.bam Biokepi_pipeline_edsl.Pipeline.t ->     Biokepi_pipeline_edsl.Pipeline.bam Biokepi_pipeline_edsl.Pipeline.t   val pair :     normal:Biokepi_pipeline_edsl.Pipeline.bam            Biokepi_pipeline_edsl.Pipeline.t ->     tumor:Biokepi_pipeline_edsl.Pipeline.bam Biokepi_pipeline_edsl.Pipeline.t ->     Biokepi_pipeline_edsl.Pipeline.bam_pair Biokepi_pipeline_edsl.Pipeline.t   val germline_variant_caller :     Biokepi_pipeline_edsl.Pipeline.germline     Biokepi_pipeline_edsl.Pipeline.Variant_caller.t ->     Biokepi_pipeline_edsl.Pipeline.bam Biokepi_pipeline_edsl.Pipeline.t ->     Biokepi_pipeline_edsl.Pipeline.vcf Biokepi_pipeline_edsl.Pipeline.t   val gatk_haplotype_caller :     Biokepi_pipeline_edsl.Pipeline.bam Biokepi_pipeline_edsl.Pipeline.t ->     Biokepi_pipeline_edsl.Pipeline.vcf Biokepi_pipeline_edsl.Pipeline.t   val somatic_variant_caller :     Biokepi_pipeline_edsl.Pipeline.somatic     Biokepi_pipeline_edsl.Pipeline.Variant_caller.t ->     Biokepi_pipeline_edsl.Pipeline.bam_pair Biokepi_pipeline_edsl.Pipeline.t ->     Biokepi_pipeline_edsl.Pipeline.vcf Biokepi_pipeline_edsl.Pipeline.t   val mutect :     ?configuration:Biokepi_bfx_tools.Mutect.Configuration.t ->     Biokepi_pipeline_edsl.Pipeline.bam_pair Biokepi_pipeline_edsl.Pipeline.t ->     Biokepi_pipeline_edsl.Pipeline.vcf Biokepi_pipeline_edsl.Pipeline.t   val mutect2 :     ?configuration:Biokepi_bfx_tools.Gatk.Configuration.Mutect2.t ->     Biokepi_pipeline_edsl.Pipeline.bam_pair Biokepi_pipeline_edsl.Pipeline.t ->     Biokepi_pipeline_edsl.Pipeline.vcf Biokepi_pipeline_edsl.Pipeline.t   val somaticsniper :     ?configuration:Biokepi_bfx_tools.Somaticsniper.Configuration.t ->     Biokepi_pipeline_edsl.Pipeline.bam_pair Biokepi_pipeline_edsl.Pipeline.t ->     Biokepi_pipeline_edsl.Pipeline.vcf Biokepi_pipeline_edsl.Pipeline.t   val varscan_somatic :     ?adjust_mapq:int ->     Biokepi_pipeline_edsl.Pipeline.bam_pair Biokepi_pipeline_edsl.Pipeline.t ->     Biokepi_pipeline_edsl.Pipeline.vcf Biokepi_pipeline_edsl.Pipeline.t   val strelka :     configuration:Biokepi_bfx_tools.Strelka.Configuration.t ->     Biokepi_pipeline_edsl.Pipeline.bam_pair Biokepi_pipeline_edsl.Pipeline.t ->     Biokepi_pipeline_edsl.Pipeline.vcf Biokepi_pipeline_edsl.Pipeline.t   val virmid :     configuration:Biokepi_bfx_tools.Virmid.Configuration.t ->     Biokepi_pipeline_edsl.Pipeline.bam_pair Biokepi_pipeline_edsl.Pipeline.t ->     Biokepi_pipeline_edsl.Pipeline.vcf Biokepi_pipeline_edsl.Pipeline.t   val muse :     configuration:Biokepi_bfx_tools.Muse.Configuration.t ->     Biokepi_pipeline_edsl.Pipeline.bam_pair Biokepi_pipeline_edsl.Pipeline.t ->     Biokepi_pipeline_edsl.Pipeline.vcf Biokepi_pipeline_edsl.Pipeline.t   val seq2hla :     Biokepi_pipeline_edsl.Pipeline.fastq_sample     Biokepi_pipeline_edsl.Pipeline.t ->     Biokepi_pipeline_edsl.Pipeline.seq2hla_hla_types     Biokepi_pipeline_edsl.Pipeline.t   val optitype :     [ `DNA | `RNA ] ->     Biokepi_pipeline_edsl.Pipeline.fastq_sample     Biokepi_pipeline_edsl.Pipeline.t ->     Biokepi_pipeline_edsl.Pipeline.optitype_hla_types     Biokepi_pipeline_edsl.Pipeline.t   val add_tags :     ?recursively:bool ->     string list ->     'a Biokepi_pipeline_edsl.Pipeline.t ->     'a Biokepi_pipeline_edsl.Pipeline.t end