modify BQSR

defaults

@@ -25,5 +25,6 @@
   "dbsnp": "dbsnp_146.hg38.vcf",
   "MENDELIANdocker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/vbt:v1.1",
   "DIYdocker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/high_confidence_call_manuscript:1.5",
-  "ref_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/"
+  "ref_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
+  "pl": "ILLUMINA"
 }

workflow.wdl

@@ -190,8 +190,8 @@ workflow {{ project_name }} {
 			input:
 			fasta=fasta,
 			ref_dir=ref_dir,
-			realigned_bam=Realigner_M8.realigner_bam,
-			realigned_bam_index=Realigner_M8.realigner_bam_index,
+			realigned_bam=Realigner_D5.realigner_bam,
+			realigned_bam_index=Realigner_D5.realigner_bam_index,
 			db_mills=db_mills,
 			dbmills_dir=dbmills_dir,
 			dbsnp=dbsnp,