修改input文件中的docker和workDir

inputs

@@ -1,5 +1,7 @@
 {
   "{{ project_name }}.TumorBam": "{{ TumorBam }}",
+  "{{ project_name }}.Tumordir": "{{ Tumordir }}",
+  "{{ project_name }}.Normaldir": "{{ Normaldir }}",
   "{{ project_name }}.TumorSampleID": "{{ TumorSampleID }}",
   "{{ project_name }}.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/cn_mops:v0.1.0",
   "{{ project_name }}.cluster_config": "OnDemand bcs.a2.3xlarge img-ubuntu-vpc",

tasks/cn_mops.wdl

@@ -1,14 +1,16 @@
 task CNV {
+	File Tumordir
 	String TumorBam
+	File Normaldir
 	String NormalBam
 	String TumorSampleID
-	String bed_file
+	File bed_file
 	String docker
 	String disk_size
 	String cluster_config
 	
 	command <<<
-		cn_mops --Tumor=${TumorBam} --Normal=${NormalBam} --TumorID==${TumorSampleID} --bed_file=${bed_file} --workDir=.
+		cn_mops --Tumor=${Tumordir}/${TumorBam} --Normal=${Normaldir}/${NormalBam} --TumorID==${TumorSampleID} --bed_file=${bed_file} --workDir=.
 	>>>
 
 	runtime {

workflow.wdl

@@ -1,23 +1,24 @@
 import "./tasks/cn_mops.wdl" as CNV
 
 workflow {{project_name}} {
-
+	File Tumordir
+	File Normaldir
 	String TumorBam
 	String NormalBam
 	String TumorSampleID
-	String bed_file
-	String workDir
+	File bed_file
 	String docker
 	String disk_size
 	String cluster_config
 
 	call CNV.CNV as CNV {
 		input: 
+			Tumordir=Tumordir,
+			Normaldir=Normaldir,
 			TumorBam=TumorBam,
 			NormalBam=NormalBam,
 			TumorSampleID=TumorSampleID,
 			bed_file=bed_file,
-			workDir=workDir,
 			docker=docker,
 			disk_size=disk_size,
 			cluster_config=cluster_config