sentieon license

defaults

@@ -1,6 +1,7 @@
 {
   "benchmarking_dir": "oss://pgx-result/renluyao/manuscript/benchmark_calls_v3.0/",
   "SENTIEON_INSTALL_DIR": "/opt/sentieon-genomics",
+  "SENTIEON_LICENSE": "192.168.0.55:8990",
   "fasta": "GRCh38.d1.vd1.fa",
   "BENCHMARKdocker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-hap:latest",
   "dbsnp_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",

inputs

@@ -1,6 +1,7 @@
 {
   "{{ project_name }}.benchmarking_dir": "{{ benchmarking_dir }}",
   "{{ project_name }}.SENTIEON_INSTALL_DIR": "{{ SENTIEON_INSTALL_DIR }}",
+  "{{ project_name }}.SENTIEON_LICENSE": "{{ SENTIEON_LICENSE }}",
   "{{ project_name }}.fasta": "{{ fasta }}",
   "{{ project_name }}.BENCHMARKdocker": "{{ BENCHMARKdocker }}",
   "{{ project_name }}.dbsnp_dir": "{{ dbsnp_dir }}",

tasks/mapping.wdl

@@ -6,6 +6,7 @@ task mapping {
 	File fastq_2
 
 	String SENTIEON_INSTALL_DIR
+	String SENTIEON_LICENSE
 	String group
 	String sample
 	String pl
@@ -16,7 +17,7 @@ task mapping {
 	command <<<
 		set -o pipefail
 		set -e	
-		export SENTIEON_LICENSE=192.168.0.55:8990
+		export SENTIEON_LICENSE=${SENTIEON_LICENSE}
 		nt=$(nproc)
 		${SENTIEON_INSTALL_DIR}/bin/bwa mem -M -R "@RG\tID:${group}\tSM:${sample}\tPL:${pl}" -t $nt -K 10000000 ${ref_dir}/${fasta} ${fastq_1} ${fastq_2} | ${SENTIEON_INSTALL_DIR}/bin/sentieon util sort -o ${sample}.sorted.bam -t $nt --sam2bam -i -
 	>>>

workflow.wdl

@@ -24,6 +24,7 @@ workflow {{ project_name }} {
 	Array[Array[File]] inputSamples = read_tsv(inputSamplesFile)
 
 	String SENTIEON_INSTALL_DIR
+	String SENTIEON_LICENSE
 	String SENTIEONdocker
 	String FASTQCdocker
 	String FASTQSCREENdocker
@@ -55,6 +56,7 @@ workflow {{ project_name }} {
 		call mapping.mapping as mapping {
 			input: 
 			SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
+			SENTIEON_LICENSE=SENTIEON_LICENSE,
 			group=quartet[2],
 			sample=quartet[2],
 			pl="ILLUMINAL",