......

defaults

@@ -2,30 +2,30 @@
     "idx": "oss://pgx-reference-data/reference/hisat2/grch38_snp_tran/",
     "gtf": "oss://pgx-reference-data/reference/annotation/Homo_sapiens.GRCh38.93.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", 
-    "fastp.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastp:0.19.6", 
-    "fastp.cluster": "OnDemand bcs.a2.large img-ubuntu-vpc", 
+    "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", 
+    "fastp_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastp:0.19.6", 
+    "fastp_cluster": "OnDemand bcs.a2.large img-ubuntu-vpc", 
     "fasta": "GRCh38.d1.vd1.fa", 
-    "fastqc.disk_size": "150", 
+    "fastqc_disk_size": "150", 
     "gtf": "oss://pgx-reference-data/reference/annotation/Homo_sapiens.GRCh38.93.gtf", 
-    "fastqscreen.cluster_config": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc",
-    "fastqc.cluster_config": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc", 
-    "qualimapBAMqc.disk_size": "500", 
-    "fastqc.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastqc:v0.11.5", 
-    "fastqscreen.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastqscreen:0.12.0", 
+    "fastqscreen_cluster_config": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc",
+    "fastqc_cluster_config": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc", 
+    "qualimapBAMqc_disk_size": "500", 
+    "fastqc_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastqc:v0.11.5", 
+    "fastqscreen_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastqscreen:0.12.0", 
     "screen_ref_dir": "oss://pgx-reference-data/fastq_screen_reference/", 
     "fastq_screen_conf": "oss://pgx-reference-data/fastq_screen_reference/fastq_screen.conf", 
-    "multiqc.cluster_config": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc", 
-    "multiqc.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/multiqc:v1.8", 
-    "qualimapBAMqc.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/qualimap:2.0.0", 
-    "qualimapBAMqc.cluster_config": "OnDemand bcs.a2.7xlarge img-ubuntu-vpc", 
-    "fastqscreen.disk_size": "100", 
-    "multiqc.disk_size": "100", 
+    "multiqc_cluster_config": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc", 
+    "multiqc_docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/multiqc:v1.8", 
+    "qualimapBAMqc_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/qualimap:2.0.0", 
+    "qualimapBAMqc_cluster_config": "OnDemand bcs.a2.7xlarge img-ubuntu-vpc", 
+    "fastqscreen_disk_size": "100", 
+    "multiqc_disk_size": "100", 
     "ref_dir": "oss://chinese-quartet/quartet-storage-data/reference_data/", 
     "trim_front1": "0", 
     "trim_tail1": "0", 

inputs

@@ -3,30 +3,30 @@
 	"{{ project_name }}.idx": "{{ idx }}",
 	"{{ project_name }}.gtf": "{{ gtf }}",
 	"{{ project_name }}.idx_prefix": "{{ idx_prefix }}",
-	"{{ project_name }}.hisat2.docker": "{{ hisat2.docker }}",
-	"{{ project_name }}.hisat2.cluster": "{{ hisat2.cluster }}",
-	"{{ project_name }}.samtools.docker": "{{ samtools.docker }}",
-	"{{ project_name }}.samtools.cluster": "{{ samtools.cluster }}",
-	"{{ project_name }}.stringtie.docker": "{{ stringtie.docker }}",
-	"{{ project_name }}.stringtie.cluster": "{{ stringtie.cluster }}",
-	"{{ project_name }}.fastp.docker": "{{ fastp.docker }}",
-	"{{ project_name }}.fastp.cluster": "{{ fastp.cluster }}",
+	"{{ project_name }}.hisat2_docker": "{{ hisat2_docker }}",
+	"{{ project_name }}.hisat2_cluster": "{{ hisat2_cluster }}",
+	"{{ project_name }}.samtools_docker": "{{ samtools_docker }}",
+	"{{ project_name }}.samtools_cluster": "{{ samtools_cluster }}",
+	"{{ project_name }}.stringtie_docker": "{{ stringtie_docker }}",
+	"{{ project_name }}.stringtie_cluster": "{{ stringtie_cluster }}",
+	"{{ project_name }}.fastp_docker": "{{ fastp_docker }}",
+	"{{ project_name }}.fastp_cluster": "{{ fastp_cluster }}",
 	"{{ project_name }}.fasta": "{{ fasta }}",
-	"{{ project_name }}.fastqc.disk_size": "{{ fastqc.disk_size }}",
+	"{{ project_name }}.fastqc_disk_size": "{{ fastqc_disk_size }}",
 	"{{ project_name }}.gtf": "{{ gtf }}",
-	"{{ project_name }}.fastqscreen.cluster_config": "{{ fastqscreen.cluster_config }}",
-	"{{ project_name }}.fastqc.cluster_config": "{{ fastqc.cluster_config }}",
-	"{{ project_name }}.qualimapBAMqc.disk_size": "{{ qualimapBAMqc.disk_size }}",
-	"{{ project_name }}.fastqc.docker": "{{ fastqc.docker }}",
-	"{{ project_name }}.fastqscreen.docker": "{{ fastqscreen.docker }}",
+	"{{ project_name }}.fastqscreen_cluster_config": "{{ fastqscreen_cluster_config }}",
+	"{{ project_name }}.fastqc_cluster_config": "{{ fastqc_cluster_config }}",
+	"{{ project_name }}.qualimapBAMqc_disk_size": "{{ qualimapBAMqc_disk_size }}",
+	"{{ project_name }}.fastqc_docker": "{{ fastqc_docker }}",
+	"{{ project_name }}.fastqscreen_docker": "{{ fastqscreen_docker }}",
 	"{{ project_name }}.screen_ref_dir": "{{ screen_ref_dir }}",
 	"{{ project_name }}.fastq_screen_conf": "{{ fastq_screen_conf }}",
-	"{{ project_name }}.multiqc.cluster_config": "{{ multiqc.cluster_config }}",
-	"{{ project_name }}.multiqc.docker": "{{ multiqc.docker }}",
-	"{{ project_name }}.qualimapBAMqc.docker": "{{ qualimapBAMqc.docker }}",
-	"{{ project_name }}.qualimapBAMqc.cluster_config": "{{ qualimapBAMqc.cluster_config }}",
-	"{{ project_name }}.fastqscreen.disk_size": "{{ fastqscreen.disk_size }}",
-	"{{ project_name }}.multiqc.disk_size": "{{ multiqc.disk_size }}",
+	"{{ project_name }}.multiqc_cluster_config": "{{ multiqc_cluster_config }}",
+	"{{ project_name }}.multiqc_docker": "{{ multiqc_docker }}",
+	"{{ project_name }}.qualimapBAMqc_docker": "{{ qualimapBAMqc_docker }}",
+	"{{ project_name }}.qualimapBAMqc_cluster_config": "{{ qualimapBAMqc_cluster_config }}",
+	"{{ project_name }}.fastqscreen_disk_size": "{{ fastqscreen_disk_size }}",
+	"{{ project_name }}.multiqc_disk_size": "{{ multiqc_disk_size }}",
 	"{{ project_name }}.ref_dir": "{{ ref_dir }}",
 	"{{ project_name }}.trim_front1": "{{ trim_front1 }}",
 	"{{ project_name }}.trim_tail1": "{{ trim_tail1 }}",

workflow.wdl

@@ -12,8 +12,8 @@ workflow {{ project_name }} {
 		sample_id=quartet[2],
 		read1=quartet[0], 
 		read2=quartet[1],
-		docker = fastp.docker,
-		cluster = fastp.cluster
+		docker = fastp_docker,
+		cluster = fastp_cluster
 		}
 	}
 }