remove threads

tasks/bcftools.wdl

@@ -9,19 +9,19 @@ task bcftools {
 	command <<<
 		set -o pipefail
 		set -e
-    nt=$(nproc)
-
+    
 		mkdir -p /cromwell_root/tmp/bcftools
 
 		for i in ${sep=" " vcf}
 		do
       echo "Processing:" $i
-			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
+      bgzip $i
+			bcftools view $i -Oz -o /cromwell_root/tmp/bcftools/$(basename $i.gz)
+			bcftools index /cromwell_root/tmp/bcftools/$(basename $i.gz) -f
 		done
 
     echo "Start bcftools merge ..."
-		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
+		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
 	>>>
 
 	runtime {