variant-calling/tasks/Realigner.wdl

task Realigner {

	File ref_dir
	File dbmills_dir

	String SENTIEON_INSTALL_DIR
	String SENTIEON_LICENSE
	String sample
	String fasta

	File? regions
	File Dedup_bam
	File Dedup_bam_index
	String db_mills
	String docker	
	String cluster_config
	String disk_size
	
	command <<<
		set -o pipefail
		set -e
		export SENTIEON_LICENSE=${SENTIEON_LICENSE}
		nt=$(nproc)
		if [ ${regions} != "" ]; then
			${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt -i ${Dedup_bam} --algo Realigner -k ${dbmills_dir}/${db_mills} --interval_list ${regions} ${sample}.sorted.deduped.realigned.bam
		else
			${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt -i ${Dedup_bam} --algo Realigner -k ${dbmills_dir}/${db_mills} ${sample}.sorted.deduped.realigned.bam
		fi		
	>>>

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

	output {
		File realigner_bam = "${sample}.sorted.deduped.realigned.bam"
		File realigner_bam_index = "${sample}.sorted.deduped.realigned.bam.bai"

	}
}