Update: TNscope.wdl

tasks/TNscope.wdl

 task TNscope {
 
-	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
-	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 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 ${corealigner_bam} --algo TNscope --tumor_sample ${tumor_name} --normal_sample ${normal_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 = "${sample}.TNscope.TN.vcf.idx"
-	}
+
+    String sample
+    String SENTIEON_INSTALL_DIR
+    String SENTIEON_LICENSE
+    File tumor_recaled_bam
+    File tumor_recaled_bam_index
+    File tumor_recal_table
+    File normal_recaled_bam
+    File normal_recaled_bam_index
+    File normal_recal_table
+    String tumor_name
+    String normal_name
+
+    File ref_dir
+    String fasta
+    File dbsnp_dir
+    String dbsnp
+    File? regions
+    
+    String docker
+    String cluster_config	
+    String disk_size
+
+    Boolean set_pon
+    File? pon_vcf
+    String pon_command = if set_pon then "--pon /cromwell_root/tmp/PON/$(basename ${pon_vcf})" else ""
+    
+    command <<<
+        set -o pipefail
+        set -e
+        export SENTIEON_LICENSE=${SENTIEON_LICENSE}
+        nt=$(nproc)
+
+        if ${set_pon}; then
+            mkdir -p /cromwell_root/tmp/PON/
+            cp ${pon_vcf} /cromwell_root/tmp/PON/
+            ${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex /cromwell_root/tmp/PON/$(basename ${pon_vcf})
+        fi
+        
+        if [ ${regions} != "" ]; then
+            ${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt \
+            --interval ${regions} -r ${ref_dir}/${fasta} \
+            -i ${tumor_recaled_bam} -q ${tumor_recal_table} \
+            -i ${normal_recaled_bam} -q ${normal_recal_table} \
+            --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} -q ${tumor_recal_table} \
+            -i ${normal_recaled_bam} -q ${normal_recal_table} \
+            --algo TNscope \
+            --tumor_sample ${tumor_name} --normal_sample ${normal_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

 	File normal_recaled_bam
 	File normal_recaled_bam_index
 	File normal_recal_table
-	File TNhaplotyper2_PoN
+	File TNseq_PoN
 	String dbsnp
 	String disk_size
 	File regions
 		export SENTIEON_LICENSE=${SENTIEON_LICENSE}
 		nt=$(nproc)
 
-		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt --interval ${regions} -r ${ref_dir}/${fasta} -i ${corealigner_bam} --algo TNhaplotyper2 --tumor_sample ${tumor_name} --normal_sample ${normal_name} --dbsnp ${dbsnp_dir}/${dbsnp} ${sample}.TNhaplotyper2.TN.vcf
+		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt --interval ${regions} -r ${ref_dir}/${fasta} -i ${corealigner_bam} --algo TNhaplotyper2 --tumor_sample ${tumor_name} --normal_sample ${normal_name} --dbsnp ${dbsnp_dir}/${dbsnp} ${sample}.TNseq.TN.vcf
 
 
 		${SENTIEON_INSTALL_DIR}/bin/sentieon driver -t $nt --interval ${regions} -r ${ref_dir}/${fasta} \
 		-i ${tumor_recaled_bam} -q ${tumor_recal_table} \
 		-i ${normal_recaled_bam} -q ${normal_recal_table} \
-		--algo TNhaplotyper2 --tumor_sample ${tumor_name} \
+		--algo TNseq --tumor_sample ${tumor_name} \
 		--normal_sample ${normal_name} \
 		--germline_vcf ${germline_resource} \
-		--pon ${TNhaplotyper2_PoN} \
-		${sample}.TNhaplotyper2.TN.tmp.vcf \
+		--pon ${TNseq_PoN} \
+		${sample}.TNseq.TN.tmp.vcf \
 		--algo OrientationBias --tumor_sample ${tumor_name} \
 		ORIENTATION_DATA \
 		--algo ContaminationModel --tumor_sample ${tumor_name} \
 		sentieon driver -r REFERENCE \
 		--algo TNfilter --tumor_sample ${tumor_name} \
 		--normal_sample ${normal_name} \
-		-v ${sample}.TNhaplotyper2.TN.tmp.vcf \
+		-v ${sample}.TNseq.TN.tmp.vcf \
 		--contamination CONTAMINATION_DATA \
 		--tumor_segments CONTAMINATION_DATA.segments \
 		--orientation_priors ORIENTATION_DATA \
-		${sample}.TNhaplotyper2.TN.vcf
+		${sample}.TNseq.TN.vcf
 	>>>
 
 	runtime {
 	}
 
 	output {
-		File TNhaplotyper2_vcf= "${sample}.TNhaplotyper2.TN.vcf"
-		File TNhaplotyper2_vcf_index = "${sample}.TNhaplotyper2.TN.vcf.idx"
+		File TNseq_vcf= "${sample}.TNseq.TN.vcf"
+		File TNseq_vcf_index = "${sample}.TNseq.TN.vcf.idx"
 	}
 
 }

workflow.wdl

             input:
             SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
             SENTIEON_LICENSE=SENTIEON_LICENSE,
-            fasta=fasta,
-            ref_dir=ref_dir,
-            regions=regions,
+            sample=sample_id,
             normal_recaled_bam=normal_BQSR.recaled_bam,
             normal_recaled_bam_index=normal_BQSR.recaled_bam_index,
             normal_recal_table=normal_BQSR.recal_table,
             tumor_recaled_bam=tumor_BQSR.recaled_bam,
             tumor_recaled_bam_index=tumor_BQSR.recaled_bam_index,
             tumor_recal_table=tumor_BQSR.recal_table,
+            normal_name=sample_id + "_normal",
+            tumor_name=sample_id + "_tumor",
+            fasta=fasta,
+            ref_dir=ref_dir,
+            regions=regions,
             dbsnp=dbsnp,
             dbsnp_dir=dbsnp_dir,
             set_pon=set_pon,
             pon_vcf=pon_vcf,
-            cosmic_vcf=cosmic_vcf,
-            cosmic_dir=cosmic_dir,
-            tumor_name=sample_id + "_tumor",
-            normal_name=sample_id + "_normal",
             docker=sentieon_docker,
-            sample=sample_id,
-            disk_size=disk_size,
-            cluster_config=cluster_config
+            cluster_config=cluster_config,
+            disk_size=disk_size
         }
 
         call annovar.annovar as TNseq_annovar {