revised workflow

defaults

@@ -1,13 +1,13 @@
 {
-  "idx": "oss://pgx-reference-data/reference/hisat2/grch38_snp_tran/", 
-  "gtf": "oss://pgx-reference-data/reference/tophat2/annotation/gencode.v22.annotation.gtf",
-  "idx_prefix": "genome_snp_tran",
-  "hisat2_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/hisat2:v2.1.0-2",
-  "hisat2_cluster": "OnDemand bcs.a2.3xlarge img-ubuntu-vpc",
-  "samtools_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/samtools:v1.3.1",
-  "samtools_cluster": "OnDemand bcs.a2.large img-ubuntu-vpc",
-  "stringtie_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/stringtie:v1.3.4",
-  "stringtie_cluster": "OnDemand bcs.a2.large img-ubuntu-vpc",
-  "ballgown_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/pgx-ballgown:0.0.1",
-  "ballgown_cluster": "OnDemand bcs.a2.large img-ubuntu-vpc"
+    "idx": "oss://pgx-reference-data/reference/hisat2/grch38_snp_tran/", 
+    "gtf": "oss://pgx-reference-data/reference/tophat2/annotation/gencode.v22.annotation.gtf",
+    "idx_prefix": "genome_snp_tran",
+    "hisat2_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/hisat2:v2.1.0-2",
+    "hisat2_cluster": "OnDemand bcs.a2.3xlarge img-ubuntu-vpc",
+    "samtools_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/samtools:v1.3.1",
+    "samtools_cluster": "OnDemand bcs.a2.large img-ubuntu-vpc",
+    "stringtie_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/stringtie:v1.3.4",
+    "stringtie_cluster": "OnDemand bcs.a2.large img-ubuntu-vpc",
+    "ballgown_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/pgx-ballgown:0.0.1",
+    "ballgown_cluster": "OnDemand bcs.a2.large img-ubuntu-vpc"
 }

workflow.wdl

@@ -10,6 +10,8 @@ workflow {{ project_name }} {
     File idx
 	String idx_prefix
     File gtf
+	String docker
+	String cluster
 	
 	
 	call hisat2.hisat2 as hisat2 {