Add threads

defaults

@@ -1,5 +1,5 @@
 {
     "bcftools_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/bcftools:v1.9",
     "disk_size": "200",
-    "cluster_config": "OnDemand bcs.a2.large img-ubuntu-vpc"
+    "cluster_config": "OnDemand bcs.a2.3xlarge img-ubuntu-vpc"
 }

tasks/bcftools.wdl

@@ -9,15 +9,17 @@ task bcftools {
 	command <<<
 		set -o pipefail
 		set -e
+    nt=$(nproc)
+
 		mkdir -p /cromwell_root/tmp/bcftools
 
 		for i in ${sep=" " vcf}
 		do
-			bcftools view $i -Oz -o /cromwell_root/tmp/bcftools/$(basename $i.gz)
-			bcftools index /cromwell_root/tmp/bcftools/$(basename $i.gz) -f
+			bcftools view $i -Oz -o /cromwell_root/tmp/bcftools/$(basename $i.gz) --threads $nt
+			bcftools index /cromwell_root/tmp/bcftools/$(basename $i.gz) -f --threads $nt
 		done
 
-		bcftools merge -m all -f PASS,. --force-samples /cromwell_root/tmp/bcftools/*.vcf.gz | bcftools plugin fill-AN-AC | bcftools filter -i 'SUM(AC)>1' > ${panel_id}_pon.vcf
+		bcftools merge -m all -f PASS,. --force-samples /cromwell_root/tmp/bcftools/*.vcf.gz --threads $nt | bcftools plugin fill-AN-AC | bcftools filter -i 'SUM(AC)>1' > ${panel_id}_pon.vcf
 	>>>
 
 	runtime {