first commit

tasks/bcftools1.wdl

@@ -12,7 +12,8 @@ task bcftools {
 		set -e
 		
 		if [ ${PONmode} ]; then
-			bcftools view ${bcfpon} -Oz -o $(basename ${bcfpon}.gz)
+			name=$(basename ${bcfpon})
+			bcftools view ${bcfpon} -Oz -o ${name}.gz
 		else
 			echo 1
 		fi