quartet_dna_quality_control_wgs_big_pipeline/tasks/merge_family.wdl

task merge_family {
	File D5_vcf
	File D6_vcf
	File F7_vcf
	File M8_vcf
	File D5_vcf_tbi
	File D6_vcf_tbi
	File F7_vcf_tbi
	File M8_vcf_tbi
	String project
	String docker
	String cluster_config
	String disk_size
	
	command <<<

		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcfmerge --force-merge-all -o ${project}.family.vcf.gz ${D5_vcf} ${D6_vcf} ${F7_vcf} ${M8_vcf}

	>>>

	runtime {
		docker:docker
		cluster: cluster_config
		systemDisk: "cloud_ssd 40"
		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
	}
	output {
		File family_vcf = "${project}.family.vcf.gz"
		File family_vcf_tbi = "${project}.family.vcf.gz.tbi"
	}
}