diffBed

inputs

@@ -1,10 +1,9 @@
 {
-  "{{ project_name }}.colSum.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/high_confidence_call_manuscript:v1.4",
+  "{{ project_name }}.diffBed.docker": "registry-internal.cn-shanghai.aliyuncs.com/pgx-docker-registry/bedtools:v2.27.1",
   "{{ project_name }}.disk_size": "200",
-  "{{ project_name }}.bedAnnotation.docker": "registry-internal.cn-shanghai.aliyuncs.com/pgx-docker-registry/bedtools:v2.27.1",
   "{{ project_name }}.inputSamplesFile": "{{ inputSamplesFile }}",
   "{{ project_name }}.sample_name": "{{ sample_name }}",
-  "{{ project_name }}.breakpoint_directory": "{{ breakpoint_directory }}",
+  "{{ project_name }}.diffBed_directory": "oss://pgx-result/renluyao/manuscript/bedregion_snp_distrubution/",
   "{{ project_name }}.cluster_config": "OnDemand bcs.a2.3xlarge img-ubuntu-vpc",
   "{{ project_name }}.mergeBed.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/high_confidence_call_manuscript:v1.4",
   "{{ project_name }}.vcf2bed.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/high_confidence_call_manuscript:v1.4"

tasks/diffBed.wdl

@@ -0,0 +1,29 @@
+task diffBed {
+	File filtered_bed
+	File voted_bed
+	File diffBed_directory
+	String sample_name
+	String docker
+	String cluster_config
+	String disk_size
+	
+	command <<<
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools annotate -counts -i ${filtered_bed} -files ${diffBed_directory}/centro_pericentro_region.bed ${diffBed_directory}/btu356_LCR-hs38.bed ${diffBed_directory}/Homopolyer.hg38.bed ${diffBed_directory}/D5.DEL ${diffBed_directory}/D5.DUP ${diffBed_directory}/D5.INV ${diffBed_directory}/sv.del.break.point.500.bed ${diffBed_directory}/sv.dup.break.point.500.bed ${diffBed_directory}/sv.ins.break.point.500.bed ${diffBed_directory}/sv.inv.break.point.1000.bed ${diffBed_directory}/sv.tra.break.point.5000.bed > ${sample_name}.diffBed.filtered.txt
+
+		/opt/ccdg/bedtools-2.27.1/bin/bedtools annotate -counts -i ${voted_bed} -files ${diffBed_directory}/centro_pericentro_region.bed ${diffBed_directory}/btu356_LCR-hs38.bed ${diffBed_directory}/Homopolyer.hg38.bed ${diffBed_directory}/D5.DEL ${diffBed_directory}/D5.DUP ${diffBed_directory}/D5.INV ${diffBed_directory}/sv.del.break.point.500.bed ${diffBed_directory}/sv.dup.break.point.500.bed ${diffBed_directory}/sv.ins.break.point.500.bed ${diffBed_directory}/sv.inv.break.point.1000.bed ${diffBed_directory}/sv.tra.break.point.5000.bed > ${sample_name}.diffBed.voted.txt
+
+
+	>>>
+
+	runtime {
+		docker:docker
+		cluster: cluster_config
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+	output {
+		File filtered_diffBed = "${sample_name}.diffBed.filtered.txt"
+		File voted_diffBed = "${sample_name}.diffBed.voted.txt"
+	}
+}

workflow.wdl

@@ -1,12 +1,14 @@
 import "./tasks/vcf2bed.wdl" as vcf2bed
 import "./tasks/mergeBed.wdl" as mergeBed
-import "./tasks/bedAnnotation.wdl" as bedAnnotation
-import "./tasks/colSum.wdl" as colSum
+#import "./tasks/bedAnnotation.wdl" as bedAnnotation
+import "./tasks/diffBed.wdl" as diffBed
+#import "./tasks/colSum.wdl" as colSum
 
 workflow {{ project_name }} {
 	File inputSamplesFile
 	Array[Array[File]] inputSamples = read_tsv(inputSamplesFile)
-	File breakpoint_directory
+#	File breakpoint_directory
+	File diffBed_directory
 	String sample_name
 	String cluster_config
 	String disk_size
@@ -30,29 +32,38 @@ workflow {{ project_name }} {
 		cluster_config=cluster_config,
 		disk_size=disk_size
 	}
-	call bedAnnotation.bedAnnotation as bedAnnotation {
+#	call bedAnnotation.bedAnnotation as bedAnnotation {
+#		input:
+#		filtered_bed=mergeBed.filtered_bed,
+#		voted_bed=mergeBed.voted_bed,
+#		breakpoint_directory=breakpoint_directory,
+#		sample_name=sample_name,
+#		cluster_config=cluster_config,
+#		disk_size=disk_size
+#	}
+	call diffBed.diffBed as diffBed{
 		input:
 		filtered_bed=mergeBed.filtered_bed,
 		voted_bed=mergeBed.voted_bed,
-		breakpoint_directory=breakpoint_directory,
-		sample_name=sample_name,
-		cluster_config=cluster_config,
-		disk_size=disk_size
-	}
-	call colSum.colSum as colSum {
-		input:
-		filtered_bnd=bedAnnotation.filtered_bnd,
-		filtered_ins=bedAnnotation.filtered_ins,
-		filtered_inv=bedAnnotation.filtered_inv,
-		filtered_del=bedAnnotation.filtered_del,
-		filtered_dup=bedAnnotation.filtered_dup,
-		voted_bnd=bedAnnotation.voted_bnd,
-		voted_ins=bedAnnotation.voted_ins,
-		voted_inv=bedAnnotation.voted_inv,
-		voted_del=bedAnnotation.voted_del,
-		voted_dup=bedAnnotation.voted_dup,
+		diffBed_directory=diffBed_directory,
 		sample_name=sample_name,
 		cluster_config=cluster_config,
 		disk_size=disk_size
 	}
+#	call colSum.colSum as colSum {ß
+#		input:
+#		filtered_bnd=bedAnnotation.filtered_bnd,
+#		filtered_ins=bedAnnotation.filtered_ins,
+#		filtered_inv=bedAnnotation.filtered_inv,
+#		filtered_del=bedAnnotation.filtered_del,
+#		filtered_dup=bedAnnotation.filtered_dup,
+#		voted_bnd=bedAnnotation.voted_bnd,
+#		voted_ins=bedAnnotation.voted_ins,
+#		voted_inv=bedAnnotation.voted_inv,
+#		voted_del=bedAnnotation.voted_del,
+#		voted_dup=bedAnnotation.voted_dup,
+#		sample_name=sample_name,
+#		cluster_config=cluster_config,
+#		disk_size=disk_size
+#	}
 }