import "./tasks/merge_mendelian_vote.wdl" as merge_mendelian_vote
import "./tasks/merge_chromo.wdl" as merge_chromo

workflow {{ project_name }} {
	File inputSamplesFile
	Array[Array[File]] inputSamples = read_tsv(inputSamplesFile)
	File mut_file
	String docker
	String sample_name
	String cluster_config
	String disk_size

	scatter (sample in inputSamples){
		call merge_mendelian_vote.merge_mendelian_vote as merge_mendelian_vote {
			input:
			vote_file=sample[0],
			mendelian_file=sample[1],
			output_prefix=sample[2],
			mut_file=mut_file,
			docker=docker,
			cluster_config=cluster_config,
			disk_size=disk_size
		}
	}
	call merge_chromo.merge_chromo as merge_chromo {
		input:
		mendelian_vote_snv=merge_mendelian_vote.mendelian_vote_snv,
		mendelian_vote_indel=merge_mendelian_vote.mendelian_vote_indel,
		sample_name=sample_name,
		docker=docker,
		cluster_config=cluster_config,
		disk_size=disk_size
	}
}