first commit

tasks/bcftools1.wdl

@@ -0,0 +1,31 @@
+task bcftools {
+
+	File bcfpon
+	String docker
+	String cluster_config
+	String disk_size
+	Boolean PONmode
+
+
+	command <<<
+		set -o pipefail
+		set -e
+		
+		if [ ${PONmode} ]; then
+			bcftools view ${bcfpon} -Oz -o $(basename ${bcfpon}.gz)
+		else
+			echo 1
+		fi
+	>>>
+
+	runtime {
+		docker: docker
+		cluster: cluster_config
+		systemDisk: "cloud_ssd 40"
+		dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+	}
+	
+	output {
+		File vcf1="$(basename ${bcfpon}.gz)"
+	}
+}

workflow.wdl

@@ -1,6 +1,6 @@
 
 import "./tasks/corealigner.wdl" as corealigner
-import "./tasks/bcftools.wdl" as bcftools
+import "./tasks/bcftools1.wdl" as bcftools
 import "./tasks/TNseq.wdl" as TNseq
 import "./tasks/TNscope.wdl" as TNscope
 import "./tasks/annovar.wdl" as annovar