add docker

inputs

@@ -4,5 +4,6 @@
   "{{ project_name }}.fq3": "{{ fq3 }}",
   "{{ project_name }}.fq_m": "{{ fq_m }}",
   "{{ project_name }}.disk_size": "{{ disk_size }}",
+  "{{ project_name }}.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/samtools:v1.3.1",
   "{{ project_name }}.cluster_config": "OnDemand bcs.a2.large img-ubuntu-vpc"
 }

tasks/mergefq.wdl

@@ -4,6 +4,7 @@ task mergefq {
 	File fq3
 	String fq_m
 	String disk_size
+	String docker
 	String cluster_config
 
 	command <<<
@@ -11,11 +12,12 @@ task mergefq {
 		if [ ! ${fq3} ]; then
 		cat ${fq1} ${fq2} > ${fq_m}
 		else
-	    cat ${fq1} ${fq2} ${fq3} > ${fq_m}
+		cat ${fq1} ${fq2} ${fq3} > ${fq_m}
 		fi
 	>>>
 
 	runtime {
+		docker: docker
 		systemDisk: "cloud_ssd 40"
 		cluster: cluster_config
 		dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"

workflow.wdl

@@ -6,6 +6,7 @@ workflow {{ project_name }} {
 	File? fq3
 	String fq_m
 	String disk_size
+	String docker
 	String cluster_config
 
 	call mergefq.mergefq as mergefq {