update

tasks/Haplotyper.wdl

-task Haplotyper {
-	
-	File ref_dir
-	File dbsnp_dir
-	
-	String SENTIEON_INSTALL_DIR
-	String SENTIEON_LICENSE
-	String fasta
-	File recaled_bam
-	File recaled_bam_index
-	File regions
-	String dbsnp
-	String sample
-	String docker
-	String cluster_config
-	String disk_size
-
-	command <<<
-		set -o pipefail
-		set -e
-		export SENTIEON_LICENSE=${SENTIEON_LICENSE}
-		nt=$(nproc)	
-		${SENTIEON_INSTALL_DIR}/bin/sentieon driver --interval ${regions} -r ${ref_dir}/${fasta} -t $nt -i ${recaled_bam} --algo Haplotyper -d ${dbsnp_dir}/${dbsnp} ${sample}_hc.vcf
-	>>>
-	
-	runtime {
-		docker: docker
-		cluster: cluster_config
-		systemDisk: "cloud_ssd 40"
-		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-	}
-
-	output {
-		File vcf = "${sample}_hc.vcf"
-		File vcf_idx = "${sample}_hc.vcf.idx"
-	}
-}
-
-

tasks/PON.wdl

-task PON {
-
-	String SENTIEON_INSTALL_DIR
-	String SENTIEON_LICENSE
-	String sample
-
-	File ref_dir
-	String fasta
-	File cosmic_dir
-	String cosmic_vcf
-	File dbsnp_dir
-	String dbsnp
-
-	File normal_recaled_bam
-	File normal_recaled_bam_index
-	String docker
-	String cluster_config
-	String disk_size
-	
-	command <<<
-		set -o pipefail
-		set -e
-		export SENTIEON_LICENSE=${SENTIEON_LICENSE}
-		nt=$(nproc)
-		mkdir -p /cromwell_root/tmp/cosmic/
-		cp ${cosmic_dir}/${cosmic_vcf} /cromwell_root/tmp/cosmic/
-		${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex /cromwell_root/tmp/cosmic/${cosmic_vcf}
-		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt -r ${ref_dir}/${fasta} -i ${normal_recaled_bam} --algo TNhaplotyper --detect_pon --cosmic /cromwell_root/tmp/cosmic/${cosmic_vcf} --dbsnp ${dbsnp_dir}/${dbsnp} ${sample}_pon.vcf
-	>>>
-	
-	runtime {
-		docker: docker
-		cluster: cluster_config
-		systemDisk: "cloud_ssd 40"
-		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"	
-	}
-
-	output {
-		File pon_vcf = "${sample}_pon.vcf"
-	}
-}

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)
-		${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} ${sample}.sorted.deduped.realigned.bam
-	>>>
-
-	runtime {
-		docker: docker
-		cluster: cluster_config
-		systemDisk: "cloud_ssd 40"
-		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-	}
-
-	output {
-		File realigner_bam = "${sample}.sorted.deduped.realigned.bam"
-		File realigner_bam_index = "${sample}.sorted.deduped.realigned.bam.bai"
-
-	}
-}
-
-

tasks/TNscope.wdl

-task TNscope {
-
-	File ref_dir
-	File dbsnp_dir
-	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 ""
-	Boolean TN = if defined(corealigner_bam) then true else false
-	
-	command <<<
-		set -o pipefail
-		set -e
-		export SENTIEON_LICENSE=${SENTIEON_LICENSE}
-		nt=$(nproc)
-
-		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})
-		
-		if ${TN}; then
-			${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt -r ${ref_dir}/${fasta} -i ${corealigner_bam} --algo TNscope --tumor_sample ${tumor_name} --normal_sample ${normal_name} --dbsnp ${dbsnp_dir}/${dbsnp} ${pon_command} ${sample}.TNscope.TN.vcf
-		else
-			${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt -r ${ref_dir}/${fasta} -i ${tumor_recaled_bam} --algo TNscope --tumor_sample ${tumor_name} --dbsnp ${dbsnp_dir}/${dbsnp} ${pon_command} ${sample}.TNscope.TN.vcf
-		fi
-		
-	>>>
-
-	runtime {
-		docker: docker
-		cluster: cluster_config
-		systemDisk: "cloud_ssd 40"
-		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-	}
-
-	output {
-		File TNscope_vcf= "${sample}.TNscope.TN.vcf"
-		File TNscope_vcf_index = "${sample}.TNscope.TN.vcf.idx"
-	}
-
-}

tasks/TNseq.wdl

-task TNseq {
-	File ref_dir
-	File dbsnp_dir
-	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 ""
-	Boolean TN = if defined(corealigner_bam) then true else false
-
-	command <<<
-		set -o pipefail
-		set -e
-		export SENTIEON_LICENSE=${SENTIEON_LICENSE}
-		nt=$(nproc)
-
-		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})
-
-		if ${TN}; then
-			${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
-		else
-			${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt -r ${ref_dir}/${fasta} -i ${tumor_recaled_bam} --algo TNhaplotyper --tumor_sample ${tumor_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"
-	}
-
-}
-
-

tasks/vcf2maf.wdl

-task vcf2maf {
-
-	File multianno_TNscope_txt
-	File multianno_TNseq_txt
-	String sample
-	String docker
-	String cluster_config
-	String disk_size
-
-	command <<<
-		vcf2maf ${multianno_TNscope_txt} ${sample}_TNscope.MAF
-		vcf2maf ${multianno_TNseq_txt} ${sample}_TNseq.MAF
-	>>>
-
-	runtime {
-		docker: docker
-		cluster: cluster_config
-		systemDisk: "cloud_ssd 40"
-		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-	}
-
-	output {
-		File tnscope_maf = "${sample}_TNscope.MAF"
-		File tnseq_maf = "${sample}_TNseq.MAF"
-	}
-}