上传文件至 ''

defaults

@@ -57,5 +57,7 @@
     "multiqc_docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/multiqc:v1.8",
     "multiqc_disk_size": "100",
     "ballgown_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/pgx-ballgown:0.0.1",
-    "ballgown_cluster": "OnDemand bcs.a2.large img-ubuntu-vpc"
+    "ballgown_cluster": "OnDemand bcs.a2.large img-ubuntu-vpc",
+    "count_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/count:v1.0",
+    "count_cluster": "OnDemand bcs.a2.large img-ubuntu-vpc"
     }

inputs

@@ -61,5 +61,7 @@
 	"{{ project_name }}.multiqc_disk_size": "{{ multiqc_disk_size }}",
 	"{{ project_name }}.ballgown_docker": "{{ ballgown_docker }}",
 	"{{ project_name }}.ballgown_cluster": "{{ ballgown_cluster }}",
-	"{{ project_name }}.disk_size": "{{ disk_size if disk_size != '' else 200}}"
+	"{{ project_name }}.disk_size": "{{ disk_size if disk_size != '' else 200}}",
+	"{{ project_name }}.count_docker": "{{ count_docker }}",
+	"{{ project_name }}.count_cluster": "{{ count_cluster }}",
 }

workflow.wdl

@@ -7,6 +7,7 @@ import "./tasks/fastqscreen.wdl" as fastqscreen
 import "./tasks/qualimapBAMqc.wdl" as qualimapBAMqc
 import "./tasks/qualimapRNAseq.wdl" as qualimapRNAseq
 import "./tasks/ballgown.wdl" as ballgown
+import "./tasks/count.wdl" as count
 
 workflow {{ project_name }} {
 	File read1
@@ -71,6 +72,8 @@ workflow {{ project_name }} {
 	String ballgown_docker
 	String ballgown_cluster
 	String disk_size
+	String count_docker
+	String count_cluster
 
 	call fastp.fastp as fastp {
 		input: 
@@ -187,4 +190,14 @@ workflow {{ project_name }} {
 		gene_abundance = stringtie.gene_abundance,
 		disk_size = disk_size
 	} 
+
+	call count.count as count {
+		input: 
+		sample_id = sample_id,
+		docker = count_docker,
+		cluster = count_cluster,
+		ballgown = stringtie.ballgown,
+		#gene_abundance = stringtie.gene_abundance,
+		disk_size = disk_size
+	} 
 }