test03

defaults

@@ -20,7 +20,6 @@
   "REPLACE_SENTIEON_DOCKER": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-replaced:1.0",
   "DEEPVARIANT_DOCKER": "xxx",
   "QUALIMAPdocker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/qualimap:2.0.0",
-  "GATK_DOCKER": "",
   "vcf_D5": "",
   "benchmark_region": "oss://pgx-result/renluyao/manuscript_v3.0/reference_datasets_v202103/Quartet.high.confidence.region.v202103.bed",
   "db_mills": "Mills_and_1000G_gold_standard.indels.hg38.vcf",

tasks/deduped_Metrics.wdl

@@ -1,7 +1,6 @@
 task deduped_Metrics {
 
     File ref_dir
-	String SENTIEON_INSTALL_DIR
 	String fasta
 	File Dedup_bam
 	File Dedup_bam_index

workflow.wdl

@@ -40,11 +40,8 @@ workflow {{ project_name }} {
 	File? vcf_F7
 	File? vcf_M8
 
-	String SENTIEON_INSTALL_DIR
-	String SENTIEON_LICENSE
 	String REPLACE_SENTIEON_DOCKER
 	String DEEPVARIANT_DOCKER
-	String SENTIEONdocker
 	String FASTQCdocker
 	String FASTQSCREENdocker
 	String QUALIMAPdocker