first commit

tasks/bcftools.wdl

@@ -21,9 +21,10 @@ task bcftools {
 			bcftools view ${pon_vcf2} -Oz -o /cromwell_root/tmp/bcftools/$(basename $pon_vcf2).gz
 			bcftools view ${pon_vcf3} -Oz -o /cromwell_root/tmp/bcftools/$(basename $pon_vcf3).gz
 			
-			bcftools index /cromwell_root/tmp/bcftools/*.vcf.gz
+			cd /cromwell_root/tmp/bcftools
+			bcftools index *.vcf.gz
 
-			bcftools merge -m all -f PASS,. --force-samples /cromwell_root/tmp/bcftools/*.vcf.gz |\ 
+			bcftools merge -m all -f PASS,. --force-samples *.vcf.gz |\ 
 			bcftools plugin fill-AN-AC |\ 
 			bcftools filter -i 'SUM(AC)>1' > panel_of_normal.vcf