fix bug

tasks/bcftools.wdl

@@ -10,16 +10,13 @@ task bcftools {
 		set -e
 		mkdir -p /cromwell_root/tmp/bcftools
 
-		echo $vcf > b
-		for i in $vcf
+		for i in ${sep=" " vcf}
 		do
 			bcftools view $i -Oz -o /cromwell_root/tmp/bcftools/$(basename $i.gz)
 			bcftools index /cromwell_root/tmp/bcftools/$(basename $i.gz) -f
 		done
 
-		ls /cromwell_root/tmp/bcftools > a
-		cd /cromwell_root/tmp/bcftools
-		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
+		bcftools merge -m all -f PASS,. --force-samples /cromwell_root/tmp/bcftools/*.vcf.gz | bcftools plugin fill-AN-AC | bcftools filter -i 'SUM(AC)>1' > panel_of_normal.vcf
 	>>>
 
 	runtime {
@@ -31,7 +28,5 @@ task bcftools {
 	
 	output {
 		File panel_of_normal_vcf = "panel_of_normal.vcf"
-		File a = "a"
-		File b = "b"
 	}
 }

tasks/bcftools1.wdl

@@ -1,28 +0,0 @@
-task bcftools {
-
-	Array[File] vcf
-	String docker
-	String cluster_config
-	String disk_size
-
-	command <<<
-		set -o pipefail
-		set -e
-		mkdir -p /cromwell_root/tmp/bcftools
-		for i in ${sep=" " vcf}
-		do
-			echo $i > b
-		done
-	>>>
-
-	runtime {
-		docker: docker
-		cluster: cluster_config
-		systemDisk: "cloud_ssd 40"
-		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
-	}
-	
-	output {
-		File b = "b"
-	}
-}

workflow.wdl

@@ -1,4 +1,4 @@
-import "./tasks/bcftools1.wdl" as bcftools
+import "./tasks/bcftools.wdl" as bcftools
 
 workflow {{ project_name }} {