benchmark_homo_ref_region/workflow.wdl

import "./tasks/gvcf_homo_ref.wdl" as gvcf_homo_ref
import "./tasks/mergeBed.wdl" as mergeBed
import "./tasks/bedVote.wdl" as bedVote
import "./tasks/collapseBed.wdl" as collapseBed


workflow {{ project_name }} {

	File inputSamplesFile
	Array[Array[File]] inputSamples = read_tsv(inputSamplesFile)
	String quartet_sample
	String disk_size
	String cluster_config
	
	scatter (quartet in inputSamples){
		call gvcf_homo_ref.gvcf_homo_ref as gvcf_homo_ref {
			input: 
			gvcf=quartet[0],
			sample=quartet[1],
			disk_size=disk_size,
			cluster_config=cluster_config
		}
	}
	call mergeBed.mergeBed as mergeBed {
		input:
		callable_bed=gvcf_homo_ref.homo_ref_bed,
		sample=quartet_sample,
		disk_size=disk_size,
		cluster_config=cluster_config
	}
	call bedVote.bedVote as bedVote {
		input:
		merged_bed=mergeBed.merged_bed,
		sample=quartet_sample,
		disk_size=disk_size,
		cluster_config=cluster_config
	}
	call collapseBed.collapseBed as collapseBed {
		input:
		bed=bedVote.consensus_bed,
		sample=quartet_sample,
		disk_size=disk_size,
		cluster_config=cluster_config
	}

}