first commit

defaults

@@ -0,0 +1,9 @@
+{
+    "regions": "oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/agilent_v6.bed",
+    "qualimapBAMqc.disk_size": "500",
+    "multiqc.cluster_config": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc",
+    "multiqc.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/multiqc:v1.8",
+    "qualimapBAMqc.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/qualimap:2.0.0",
+    "qualimapBAMqc.cluster_config": "OnDemand bcs.a2.7xlarge img-ubuntu-vpc",
+    "multiqc.disk_size": "100"
+}

inputs

@@ -1,9 +1,10 @@
 {
-  "{{ project_name }}.qualimapBAMqc.disk_size": "500",
+  "{{ project_name }}.qualimapBAMqc.disk_size": "{{ qualimapBAMqc.disk_size }}",
   "{{ project_name }}.inputSamplesFile": "{{ inputSamplesFile }}",
-  "{{ project_name }}.multiqc.cluster_config": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc",
-  "{{ project_name }}.multiqc.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/multiqc:v1.8",
-  "{{ project_name }}.qualimapBAMqc.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/qualimap:2.0.0",
-  "{{ project_name }}.qualimapBAMqc.cluster_config": "OnDemand bcs.a2.7xlarge img-ubuntu-vpc",
-  "{{ project_name }}.multiqc.disk_size": "100"
+  "{{ project_name }}.multiqc.cluster_config": "{{ multiqc.cluster_config }}",
+  "{{ project_name }}.multiqc.docker": "{{ multiqc.docker }}",
+  "{{ project_name }}.qualimapBAMqc.docker": "{{ qualimapBAMqc.docker }}",
+  "{{ project_name }}.qualimapBAMqc.cluster_config": "{{ qualimapBAMqc.cluster_config }}",
+  "{{ project_name }}.regions": "{{ regions }}",
+  "{{ project_name }}.multiqc.disk_size": "{{ multiqc.disk_size }}"
 }

tasks/qualimapBAMqc.wdl

@@ -1,6 +1,7 @@
 task qualimapBAMqc {
 	File bam
 	File bai
+	File regions
 	String bamname = basename(bam,".bam")
 	String docker
 	String cluster_config
@@ -10,7 +11,7 @@ task qualimapBAMqc {
 		set -o pipefail
 		set -e
 		nt=$(nproc)
-		/opt/qualimap/qualimap bamqc -bam ${bam} -outformat PDF:HTML -nt $nt -outdir ${bamname}_bamqc --java-mem-size=32G 
+		/opt/qualimap/qualimap bamqc -bam ${bam} -regions ${regions} -outformat PDF:HTML -nt $nt -outdir ${bamname}_bamqc --java-mem-size=32G 
 		tar -zcvf ${bamname}_bamqc_qualimap.zip ${bamname}_bamqc
 	>>>
 

workflow.wdl

@@ -4,6 +4,7 @@ import "./tasks/multiqc.wdl" as multiqc
 workflow {{ project_name }} {
 
 	File inputSamplesFile
+	File regions
 	Array[Array[File]] inputSamples = read_tsv(inputSamplesFile)
 
 	scatter (sample in inputSamples) {
@@ -18,6 +19,7 @@ workflow {{ project_name }} {
 	call multiqc.multiqc as multiqc {
 		input:
 		bamqc_zip=qualimapBAMqc.bamqc_zip
+		regions=regions
 	}
 
 }