quartet-wgs-germline-data-generation-qc/tasks/vcfstat.wdl

task vcfstat {
	File rtg_vcf
	File rtg_vcf_index
	String sample_name
	String docker
	String cluster_config
	String disk_size

	command <<<
		set -o pipefail
		set -e

		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcfstats ${rtg_vcf} > ${sample_name}.stats.txt
	>>>

	runtime {
		docker:docker
    	cluster:cluster_config
    	systemDisk:"cloud_ssd 40"
    	dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"
	}
	output {
		File vcfnumber="${sample_name}.stats.txt"
	}
}