fix bug

tasks/bcftools.wdl

@@ -8,32 +8,16 @@ task bcftools {
 	command <<<
 		set -o pipefail
 		set -e
-
 		mkdir -p /cromwell_root/tmp/bcftools
 
 		for i in ${sep=" " bcfpon}
 		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 $i.gz)
+			bcftools index /cromwell_root/tmp/bcftools/$(basename $i.gz) -f
 		done
 
 		cd /cromwell_root/tmp/bcftools
 		bcftools merge -m all -f PASS,. --force-samples *.gz | bcftools plugin fill-AN-AC | bcftools filter -i 'SUM(AC)>1' > panel_of_normal.vcf
-			#mkdir -p /cromwell_root/tmp/bcftools
-			#bcftools view ${pon_vcf1} -Oz -o /cromwell_root/tmp/bcftools/$(basename ${pon_vcf1}.gz)
-			#bcftools view ${pon_vcf2} -Oz -o /cromwell_root/tmp/bcftools/$(basename ${pon_vcf1}.gz)
-			#bcftools view ${pon_vcf3} -Oz -o /cromwell_root/tmp/bcftools/$(basename ${pon_vcf1}.gz)
-			#cd /cromwell_root/tmp/bcftools
-			#bcftools view ${pon_vcf1} -Oz -o $(basename ${pon_vcf1}.gz)
-			#bcftools view ${pon_vcf2} -Oz -o $(basename ${pon_vcf2}.gz)
-			#bcftools view ${pon_vcf2} -Oz -o $(basename ${pon_vcf3}.gz)
-
-			#for i in `ls *.gz`; do bcftools index $i -f; done
-			#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
-		#else
-		#	echo 1
-			#touch panel_of_normal.vcf
-		#fi
 	>>>
 
 	runtime {
@@ -44,10 +28,6 @@ task bcftools {
 	}
 	
 	output {
-		File vcf1="$(basename ${bcfpon}.gz)"
-		#File vcf1="$(basename ${pon_vcf1}.gz)"
-		#File vcf2="$(basename ${pon_vcf2}.gz)"
-		#File vcf3="$(basename ${pon_vcf3}.gz)"
-		#File panel_of_normal_vcf = "panel_of_normal.vcf"
+		File panel_of_normal_vcf = "panel_of_normal.vcf"
 	}
 }