bcftools-merge/tasks/corealigner.wdl

task corealigner {
	
	File ref_dir
	File dbsnp_dir
	File dbmills_dir

	Array[String] sample
	String SENTIEON_INSTALL_DIR
	String SENTIEON_LICENSE
	String docker
	String cluster_config
	String fasta

	String dbsnp
	String db_mills
	Array[File] tumor_recaled_bam
	Array[File] tumor_recaled_bam_index
	Array[File] normal_recaled_bam
	Array[File] normal_recaled_bam_index
	String disk_size


	command <<<
		set -o pipefail
		set -e
		export SENTIEON_LICENSE=${SENTIEON_LICENSE}
		nt=$(nproc)
		#${sep=" " tumor_recaled_bam}
		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -r ${ref_dir}/${fasta} -t $nt -i ${sep=" -i " tumor_recaled_bam} -i ${sep=" -i " normal_recaled_bam} --algo Realigner -k ${dbmills_dir}/${db_mills} -k ${dbsnp_dir}/${dbsnp} ${sep=" " sample}_corealigned.bam				
	>>>
	
	runtime {
		docker: docker
		cluster: cluster_config
		systemDisk: "cloud_ssd 40"
		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
	}

	output {
		File corealigner_bam = "${sep=" " sample}_corealigned.bam"
		File corealigner_bam_index = "${sep=" " sample}_corealigned.bam.bai"
	}	
}