concatVCF/tasks/merge.wdl

task merge {
	File snv_gzvcf_2
	File indel_gzvcf_2
	File snv_gzvcf_index
	File indel_gzvcf_index
	String sample
	String docker
	String cluster_config
	String disk_size
	
	command <<<
		/opt/hall-lab/bcftools-1.9/bin/bcftools concat -a ${snv_gzvcf_2} ${indel_gzvcf_2} > ${sample}.vcf
	>>>

	runtime {
		docker:docker
		cluster: cluster_config
		systemDisk: "cloud_ssd 40"
		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
	}
	output {
		File vcf = "${sample}.vcf"
	}
}