bedtools

inputs

@@ -1,11 +1,11 @@
 {
-  "{{ project_name }}.fasta": "String",
-  "{{ project_name }}.disk_size": "String",
-  "{{ project_name }}.inputSamplesFile": "File",
-  "{{ project_name }}.bedVote.docker": "String",
-  "{{ project_name }}.cluster_config": "String",
-  "{{ project_name }}.mergeBed.docker": "String",
-  "{{ project_name }}.CallableLoci.docker": "String",
-  "{{ project_name }}.sample": "String",
-  "{{ project_name }}.ref_dir": "File"
+  "{{ project_name }}.fasta": "GRCh38.d1.vd1.fa",
+  "{{ project_name }}.disk_size": "150",
+  "{{ project_name }}.inputSamplesFile": "{{ inputSamplesFile }}",
+  "{{ project_name }}.bedVote.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/high_confidence_call_manuscript:v1.1",
+  "{{ project_name }}.cluster_config": "OnDemand bcs.b4.xlarge img-ubuntu-vpc",
+  "{{ project_name }}.mergeBed.docker": "registry-internal.cn-shanghai.aliyuncs.com/pgx-docker-registry/bedtools:v2.27.1",
+  "{{ project_name }}.CallableLoci.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/gatk:3.8-1",
+  "{{ project_name }}.sample": "{{ sample }}",
+  "{{ project_name }}.ref_dir": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/high_confidence_call_manuscript:v1.1"
 }

tasks/mergeBed.wdl

@@ -9,7 +9,7 @@ task mergeBed {
 
 	command <<<
 		
-		bedtools multiinter -i ${sep=" " callable_bed} > ${sample}.CALLABLE.bed
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools multiinter -i ${sep=" " callable_bed} > ${sample}.CALLABLE.bed
 
 		>>>