first commit

tasks/bcftools.wdl

@@ -14,13 +14,16 @@ task bcftools {
 		set -e
 		
 		if [ ${PONmode} ]; then
-			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
-			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
+			#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
 			touch panel_of_normal.vcf
 		fi
@@ -34,6 +37,9 @@ task bcftools {
 	}
 	
 	output {
-		File panel_of_normal_vcf = "panel_of_normal.vcf"
+		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"
 	}
 }