Add annotation

tasks/bcftools.wdl

@@ -15,10 +15,12 @@ task 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
 		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
 	>>>