test02

defaults

@@ -17,7 +17,7 @@
   "FASTQSCREENdocker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastqscreen:0.12.0",
   "SENTIEON_LICENSE": "192.168.0.55:8990",
   "SENTIEONdocker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v2019.11.28",
-  "REPLACE_SENTIEON_DOCKER": "xxx",
+  "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": "",

workflow.wdl

@@ -183,35 +183,35 @@ workflow {{ project_name }} {
 			cluster_config=BIGcluster_config
 		}
 
-		call Haplotyper.Haplotyper as Haplotyper_D5 {
-			input:
-			fasta=fasta,
-			ref_dir=ref_dir,
-			recaled_bam=BQSR_D5.recaled_bam,
-			recaled_bam_index=BQSR_D5.recaled_bam_index,
-			docker=DEEPVARIANT_DOCKE,
-			disk_size=disk_size,
-			cluster_config=BIGcluster_config
-		}
+		# call Haplotyper.Haplotyper as Haplotyper_D5 {
+		# 	input:
+		# 	fasta=fasta,
+		# 	ref_dir=ref_dir,
+		# 	recaled_bam=BQSR_D5.recaled_bam,
+		# 	recaled_bam_index=BQSR_D5.recaled_bam_index,
+		# 	docker=DEEPVARIANT_DOCKE,
+		# 	disk_size=disk_size,
+		# 	cluster_config=BIGcluster_config
+		# }
 
-		call filter_vcf.filter_vcf as filter_vcf_D5 {
-			input:
-			vcf=Haplotyper_D5.vcf,
-			docker=BEDTOOLSdocker,
-			cluster_config=SMALLcluster_config,
-			disk_size=disk_size			
-		}
+		# call filter_vcf.filter_vcf as filter_vcf_D5 {
+		# 	input:
+		# 	vcf=Haplotyper_D5.vcf,
+		# 	docker=BEDTOOLSdocker,
+		# 	cluster_config=SMALLcluster_config,
+		# 	disk_size=disk_size			
+		# }
 
-		call benchmark.benchmark as benchmark_D5 {
-			input:
-			filtered_vcf=filter_vcf_D5.filtered_vcf,
-			benchmarking_dir=benchmarking_dir,
-			ref_dir=ref_dir,
-			fasta=fasta,
-			docker=BENCHMARKdocker,
-			cluster_config=BIGcluster_config,
-			disk_size=disk_size
-		}		
+		# call benchmark.benchmark as benchmark_D5 {
+		# 	input:
+		# 	filtered_vcf=filter_vcf_D5.filtered_vcf,
+		# 	benchmarking_dir=benchmarking_dir,
+		# 	ref_dir=ref_dir,
+		# 	fasta=fasta,
+		# 	docker=BENCHMARKdocker,
+		# 	cluster_config=BIGcluster_config,
+		# 	disk_size=disk_size
+		# }		
 
 		# call mapping.mapping as mapping_D6 {
 		# 	input: