collapse bed

inputs

@@ -1,5 +1,6 @@
 {
   "{{ project_name }}.disk_size": "500",
+  "{{ project_name }}.collapseBed.docker": "registry-internal.cn-shanghai.aliyuncs.com/pgx-docker-registry/bedtools:v2.27.1",
   "{{ 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.ps.g.xlarge img-ubuntu-vpc",
@@ -7,4 +8,3 @@
   "{{ project_name }}.gvcf_homo_ref.docker": "registry-internal.cn-shanghai.aliyuncs.com/pgx-docker-registry/bedtools:v2.27.1",
   "{{ project_name }}.quartet_sample": "{{ quartet_sample }}"
 }
-

tasks/bedVote.wdl

@@ -11,6 +11,8 @@ task bedVote {
 		
 		python /opt/callable_bed_voting.py -bed ${merged_bed} -prefix ${sample}
 
+		cat ${sample}.27consensus.bed | cut -f1-3 > ${sample}.27consensus.temp.bed 
+
 		>>>
 
 		runtime {

tasks/collapseBed.wdl

@@ -0,0 +1,32 @@
+task collapseBed {
+	
+	File bed
+	String sample
+	String docker
+	String disk_size
+	String cluster_config
+	
+
+	command <<<
+
+		cat ${bed} | cut -f1-3 > ${sample}.temp.bed
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools merge -i ${sample}.temp.bed > ${sample}.27.homo_ref.consensus.bed
+
+		>>>
+
+		runtime {
+		docker:docker
+    	cluster:cluster_config
+    	systemDisk: "cloud_ssd 40"
+    	dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+
+	output {
+		File merged_homo_ref_bed = "${sample}.27.homo_ref.consensus.bed"
+	}
+}
+
+
+
+

workflow.wdl

@@ -1,6 +1,7 @@
 import "./tasks/gvcf_homo_ref.wdl" as gvcf_homo_ref
 import "./tasks/mergeBed.wdl" as mergeBed
 import "./tasks/bedVote.wdl" as bedVote
+import "./tasks/collapseBed.wdl" as collapseBed
 
 
 workflow {{ project_name }} {
@@ -34,5 +35,13 @@ workflow {{ project_name }} {
 		disk_size=disk_size,
 		cluster_config=cluster_config
 	}
+	call collapseBed.collapseBed as collapseBed {
+		input:
+		bed=bedVote.consensus_bed,
+		sample=quartet_sample,
+		disk_size=disk_size,
+		cluster_config=cluster_config
+	}
+
 }