import "./tasks/vcf2bed.wdl" as vcf2bed
import "./tasks/mergeBed.wdl" as mergeBed
#import "./tasks/bedAnnotation.wdl" as bedAnnotation
import "./tasks/diffBed.wdl" as diffBed
#import "./tasks/colSum.wdl" as colSum

workflow {{ project_name }} {
	File inputSamplesFile
	Array[Array[File]] inputSamples = read_tsv(inputSamplesFile)
#	File breakpoint_directory
	File diffBed_directory
	String sample_name
	String cluster_config
	String disk_size

	scatter (sample in inputSamples){
		call vcf2bed.vcf2bed as vcf2bed {
			input:
			vcf=sample[0],
			vote_file=sample[1],
			chromo=sample[2],
			sample_name=sample_name,
			cluster_config=cluster_config,
			disk_size=disk_size	
		}
	}
	call mergeBed.mergeBed as mergeBed {
		input:
		chromo_filtered_bed=vcf2bed.chromo_filtered_bed,
		chromo_voted_bed=vcf2bed.chromo_voted_bed,
		sample_name=sample_name,
		cluster_config=cluster_config,
		disk_size=disk_size
	}
#	call bedAnnotation.bedAnnotation as bedAnnotation {
#		input:
#		filtered_bed=mergeBed.filtered_bed,
#		voted_bed=mergeBed.voted_bed,
#		breakpoint_directory=breakpoint_directory,
#		sample_name=sample_name,
#		cluster_config=cluster_config,
#		disk_size=disk_size
#	}
	call diffBed.diffBed as diffBed{
		input:
		filtered_bed=mergeBed.filtered_bed,
		voted_bed=mergeBed.voted_bed,
		diffBed_directory=diffBed_directory,
		sample_name=sample_name,
		cluster_config=cluster_config,
		disk_size=disk_size
	}
#	call colSum.colSum as colSum {ß
#		input:
#		filtered_bnd=bedAnnotation.filtered_bnd,
#		filtered_ins=bedAnnotation.filtered_ins,
#		filtered_inv=bedAnnotation.filtered_inv,
#		filtered_del=bedAnnotation.filtered_del,
#		filtered_dup=bedAnnotation.filtered_dup,
#		voted_bnd=bedAnnotation.voted_bnd,
#		voted_ins=bedAnnotation.voted_ins,
#		voted_inv=bedAnnotation.voted_inv,
#		voted_del=bedAnnotation.voted_del,
#		voted_dup=bedAnnotation.voted_dup,
#		sample_name=sample_name,
#		cluster_config=cluster_config,
#		disk_size=disk_size
#	}
}