VCF_QC/tasks/filtered.wdl

task filtered {
	File raw_vcf
	File del_bed
	String family_name = basename(raw_vcf,".family.vcf")
	String docker
	String cluster_config
	String disk_size

	command <<<
		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg bgzip ${raw_vcf} -c > ${family_name}.rtg.vcf.gz
		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg index -f vcf ${family_name}.rtg.vcf.gz

		/opt/rtg-tools/dist/rtg-tools-3.10.1-4d58ead/rtg vcffilter -i ${family_name}.rtg.vcf.gz -o ${family_name}.noDEL.vcf.gz --exclude-bed=${del_bed}

		gunzip ${family_name}.noDEL.vcf.gz
	>>>

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