Update: Add Old TNseq

tasks/TNseqold.wdl

@@ -21,48 +21,44 @@ task TNseqold {
   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)
 
-	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
 
-		if [ ${regions} ]; then
-		INTERVAL="--interval ${regions} --interval_padding ${interval_padding}"
-		else
-		INTERVAL=""
-		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.old.TN.vcf
+  >>>
 
-		if [ ${pon_vcf} ]; then
-		PON="--pon ${pon_vcf}"
-		${SENTIEON_INSTALL_DIR}/bin/sentieon util vcfindex ${pon_vcf}
-		else
-		PON=""
-		fi
+  runtime {
+    docker: docker
+    cluster: cluster_config
+    systemDisk: "cloud_ssd 40"
+    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+  }
 
-		${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 = "${sample}.TNseq.old.TN.vcf.idx"
-	}
+  output {
+    File TNseq_vcf= "${sample}.TNseq.old.TN.vcf"
+    File TNseq_vcf_index = "${sample}.TNseq.old.TN.vcf.idx"
+  }

workflow.wdl

@@ -71,10 +71,10 @@ workflow {{ project_name }} {
       disk_size=disk_size
     }
 
-    call annovar.annovar as TNseq_annovar {
+    call annovar.annovar as TNseqold_annovar {
     input:
       sample=sample_id,
-      vcf=TNseq.TNseq_vcf,
+      vcf=TNseqold.TNseq_vcf,
       database=database,
       docker=annovar_docker,
       cluster_config=cluster_config,