Update: Add Old TNseq

defaults

@@ -24,7 +24,8 @@
     "disk_size": "200",
     "cluster_config": "OnDemand bcs.a2.3xlarge img-ubuntu-vpc",
     "germline": false,
-    "tnseq": true,
-    "tnscope": true,
-    "varscan": true
+    "tnseq": false,
+    "tnscope": false,
+    "varscan": false,
+    "tnseqold": false
 }

inputs

@@ -31,6 +31,7 @@
   "{{ project_name }}.cluster_config": "{{ cluster_config }}",
   "{{ project_name }}.germline": {{ germline | tojson }},
   "{{ project_name }}.tnseq": {{ tnseq | tojson }},
+  "{{ project_name }}.tnseqold": {{ tnseqold | tojson }},
   "{{ project_name }}.tnscope": {{ tnscope | tojson }},
   "{{ project_name }}.varscan": {{ varscan | tojson }}
 }

tasks/TNseqold.wdl

@@ -0,0 +1,68 @@
+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"
+	}

workflow.wdl

@@ -1,4 +1,5 @@
 import "./tasks/TNseq.wdl" as TNseq
+import "./tasks/TNseqold.wdl" as TNseqold
 import "./tasks/TNscope.wdl" as TNscope
 import "./tasks/annovar.wdl" as annovar
 
@@ -42,9 +43,45 @@ workflow {{ project_name }} {
 
   Boolean germline
   Boolean tnseq
+  Boolean tnseqold
   Boolean tnscope
   Boolean varscan
 
+  if (tnseqold) {
+    call TNseqold.TNseqold as TNseqold {
+      input:
+      SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+      SENTIEON_LICENSE=SENTIEON_LICENSE,
+      sample=sample_id,
+      normal_recaled_bam=normal_bam,
+      normal_recaled_bam_index=normal_bai,
+      normal_recal_table=normal_table,
+      tumor_recaled_bam=tumor_bam,
+      tumor_recaled_bam_index=tumor_bai,
+      tumor_recal_table=tumor_table,
+      normal_name=sample_id + "_normal",
+      tumor_name=sample_id + "_tumor",
+      fasta=fasta,
+      ref_dir=ref_dir,
+      regions=regions,
+      interval_padding=interval_padding,
+      pon_vcf=tnseq_pon,
+      docker=sentieon_docker,
+      cluster_config=cluster_config,
+      disk_size=disk_size
+    }
+
+    call annovar.annovar as TNseq_annovar {
+    input:
+      sample=sample_id,
+      vcf=TNseq.TNseq_vcf,
+      database=database,
+      docker=annovar_docker,
+      cluster_config=cluster_config,
+      disk_size=disk_size
+    }
+  }
+
   if (tnseq) {
     call TNseq.TNseq as TNseq {
       input: