variant-calling/tasks/TNseq.wdl

task TNseq {
	File ref_dir
	File dbsnp_dir
	File? regions
	String sample
	String SENTIEON_INSTALL_DIR
	String SENTIEON_LICENSE
	String tumor_name
	String normal_name
	String docker
	String cluster_config

	String fasta
	File? corealigner_bam
	File? corealigner_bam_index
	File tumor_recaled_bam
	File tumor_recaled_bam_index
	String dbsnp
	String disk_size

	Boolean set_pon
	String? cosmic_vcf
	File? cosmic_dir
	File? pon_vcf
	
	String pon_command = if set_pon then "--pon /cromwell_root/tmp/PON/$(basename ${pon_vcf}) --cosmic /cromwell_root/tmp/PON/${cosmic_vcf}" else ""

	command <<<
		set -o pipefail
		set -e
		export SENTIEON_LICENSE=${SENTIEON_LICENSE}
		nt=$(nproc)

		if ${set_pon}; then
			mkdir -p /cromwell_root/tmp/PON/
			cp ${cosmic_dir}/${cosmic_vcf} /cromwell_root/tmp/PON/
			cp ${pon_vcf} /cromwell_root/tmp/PON/
			${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex /cromwell_root/tmp/PON/${cosmic_vcf}
			${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex /cromwell_root/tmp/PON/$(basename ${pon_vcf})
		fi
		
		if [ ${regions} != "" ]; then
			${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt --interval ${regions} -r ${ref_dir}/${fasta} -i ${corealigner_bam} --algo TNhaplotyper --tumor_sample ${tumor_name} --normal_sample ${normal_name} --dbsnp ${dbsnp_dir}/${dbsnp} ${pon_command} ${sample}.TNseq.TN.vcf
		else
			${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt -r ${ref_dir}/${fasta} -i ${corealigner_bam} --algo TNhaplotyper --tumor_sample ${tumor_name} --normal_sample ${normal_name} --dbsnp ${dbsnp_dir}/${dbsnp} ${pon_command} ${sample}.TNseq.TN.vcf
		fi
	>>>

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

	output {
		File TNseq_vcf= "${sample}.TNseq.TN.vcf"
		File TNseq_vcf_index = "${sample}.TNseq.TN.vcf.idx"
	}
}