revised-bedtools-task

inputs

@@ -4,4 +4,6 @@
   "{{ project_name }}.bedtools.cluster_config": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc",
   "{{ project_name }}.bedtools.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/bedtools:v2.27.1",
   "{{ project_name }}.bedtools.disk_size": "{{disk_size}}"
+  "{{ project_name }}.cp_bam.cluster_config": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc",
+  "{{ project_name }}.cp_bam.disk_size": "{{disk_size}}"
 }

tasks/cp_bam.wdl

@@ -1,10 +1,8 @@
 task cp_bam {
 
 	File bam
-	File bai
     String bamname = basename(bam,".bam")
 
-	String docker
 	String cluster_config
 	String disk_size
 
@@ -14,7 +12,6 @@ task cp_bam {
 	>>>
 
 	runtime {
-		docker:docker
 		cluster:cluster_config
 		systemDisk:"cloud_ssd 40"
 		dataDisk:"cloud_ssd " + disk_size + " /cromwell_root/"

workflow.wdl

@@ -11,7 +11,6 @@ workflow {{ project_name }} {
 		call cp_bam.cp_bam as cp_bam {
 			input:
 			bam=sample[0]
-
 		}
 
 		call bedtools.bedtools as bedtools {