first-commit

inputs

@@ -3,5 +3,5 @@
   "{{ project_name }}.bed_file": "oss://pgx-reference-data/reference/bedtools/ERVmap_v2_all_sorted.bed", 
   "{{ 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": "100"
+  "{{ project_name }}.bedtools.disk_size": "{{disk_size}}"
 }

tasks/bedtools.wdl

@@ -9,9 +9,7 @@ task bedtools {
 	String disk_size
 
 	command <<<
-		set -o pipefail
-		set -e
-		
+			
 		bedtools multicov -bams ${bam} -bed ${bed_file} > revread_count.txt 
 	
 	>>>