update workflow

inputs

@@ -2,7 +2,7 @@
   "{{ project_name }}.sample_id": "{{ sample_id }}",
   "{{ project_name }}.bam": "{{ bam }}",
   "{{ project_name }}.bai": "{{ bai }}",
-  "{{ project_name }}.regions": "{{ regions }}",
+  "{{ project_name }}.bed": "{{ bed }}",
   "{{ project_name }}.disk_size": "{{ disk_size }}",
   "{{ project_name }}.count_docker": "{{ count_docker }}",
   "{{ project_name }}.samtools_docker": "{{ samtools_docker }}",

tasks/count.wdl

@@ -2,13 +2,13 @@ task count {
 
     String sample_id
     File readcount
-    File regions
+    File bed
     String docker
     String cluster_config
     String disk_size
-	
+
     command <<<
-        python /count.py -s ${sample_id} -i ${readcount} -c ${regions} -o ${sample_id}.coverage
+        python /count.py -s ${sample_id} -i ${readcount} -c ${bed} -o ${sample_id}.coverage
     >>>
 
     runtime {

tasks/depth.wdl

@@ -2,13 +2,13 @@ task depth {
 	File bam
 	File bai
 	String sample_id
-	File regions
+	File bed
 	String docker
 	String cluster_config
 	String disk_size
 	
 	command <<<
-		/opt/conda/bin/samtools depth -b ${regions} ${bam} > ${sample_id}.depth
+		/opt/conda/bin/samtools depth -b ${bed} ${bam} > ${sample_id}.depth
 	>>>
 
 	runtime {

workflow.wdl

@@ -1,11 +1,11 @@
 import "./tasks/depth.wdl" as depth
-import "./tasks/count.wdl" as depth
+import "./tasks/count.wdl" as count
 
 workflow {{ project_name }} {
 	File bam
 	File bai
 	String sample_id
-	File regions
+	File bed
 	String samtools_docker
 	String count_docker
 	String cluster_config
@@ -16,7 +16,7 @@ workflow {{ project_name }} {
 		bam=bam,
 		bai=bai,
 		sample_id=sample_id,
-		regions=regions,
+		bed=bed,
 		docker=samtools_docker,
 		cluster_config=cluster_config,
 		disk_size=disk_size
@@ -25,7 +25,7 @@ workflow {{ project_name }} {
     call count.count as count {
         input:
         readcount=depth.bam_depth,
-        regions=regions,
+        bed=bed,
         docker=count_docker,
         disk_size=disk_size,
         cluster_config=cluster_config,