Varscan2/tasks/vcf2maf.wdl

task vcf2maf {

	File multianno_varscan_snp_txt
	File multianno_varscan_indel_txt
	String sample
	String docker
	String cluster_config
	String disk_size

	command <<<
		vcf2maf ${multianno_varscan_snp_txt} ${sample}_varscan_snp.MAF
		vcf2maf ${multianno_varscan_indel_txt} ${sample}_varscan_indel.MAF
	>>>

	runtime {
		docker: docker
		cluster: cluster_config
		systemDisk: "cloud_ssd 40"
		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
	}

	output {
		File varscan_snp_maf = "${sample}_varscan_snp.MAF"
		File varscan_indel_maf = "${sample}_varscan_indel.MAF"
	}
}