first commit

defaults

@@ -0,0 +1,3 @@
+{
+    "regions": "oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/agilent_v6.bed"    
+}

inputs

@@ -21,5 +21,6 @@
   "{{ project_name }}.mergeSentieon.cluster_config": "OnDemand bcs.a2.large img-ubuntu-vpc",
   "{{ project_name }}.fastqscreen.disk_size": "100",
   "{{ project_name }}.multiqc.disk_size": "100",
+  "{{ project_name }}.regions": "{{ regions }}",
   "{{ project_name }}.ref_dir": "oss://chinese-quartet/quartet-storage-data/reference_data/"
 }

tasks/qualimap.wdl

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

workflow.wdl

@@ -10,6 +10,7 @@ workflow {{ project_name }} {
 	File screen_ref_dir
 	File fastq_screen_conf
 	File ref_dir
+	File regions
 	String fasta
 
 	scatter (sample in inputSamples) {
@@ -29,6 +30,7 @@ workflow {{ project_name }} {
 
 		call qualimap.qualimap as qualimap {
 			input:
+			regions=regions,
 			bam=sample[2],
 			bai=sample[3]
 		}