caller-test/tasks/TNseqold.wdl

task TNseqold {

  String sample
  String SENTIEON_INSTALL_DIR
  String SENTIEON_LICENSE
  File tumor_recaled_bam
  File tumor_recaled_bam_index
  File tumor_recal_table
  File normal_recaled_bam
  File normal_recaled_bam_index
  File normal_recal_table
  String tumor_name
  String normal_name

  File ref_dir
  String fasta
  File? regions
  Int? interval_padding
  File? pon_vcf

  String docker
  String cluster_config  
  String disk_size
	
	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 [ ${regions} ]; then
		INTERVAL="--interval ${regions} --interval_padding ${interval_padding}"
		else
		INTERVAL=""
		fi

		if [ ${pon_vcf} ]; then
		PON="--pon ${pon_vcf}"
		${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex ${pon_vcf}
		else
		PON=""
		fi

		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt \
		--INTERVAL -r ${ref_dir}/${fasta} \
		-i ${tumor_recaled_bam} -q ${tumor_recal_table} \
		-i ${normal_recaled_bam} -q ${normal_recal_table} \
		--algo TNhaplotyper \
		--tumor_sample ${tumor_name} --normal_sample ${normal_name} \
		--dbsnp ${dbsnp_dir}/${dbsnp} $PON \
		${sample}.TNseq.TN.vcf
		
	>>>

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

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