fix vcfstats

biopet.wdl

@@ -425,7 +425,7 @@ task VcfStats {
         File refFasta
         File refFastaIndex
         File refDict
-        String outDir
+        String outputDir
         File? intervals
         Array[String]+? infoTags
         Array[String]+? genotypeTags
@@ -455,11 +455,12 @@ task VcfStats {
 
     command {
         set -e -o pipefail
+        mkdir -p ~{outputDir}
         ~{preCommand}
         ~{toolCommand} \
         -I ~{vcfFile} \
         -R ~{refFasta} \
-        -o ~{outDir} \
+        -o ~{outputDir} \
         -t ~{localThreads} \
         ~{"--intervals " + intervals} \
         ~{true="--infoTag" false="" defined(infoTags)} ~{sep=" --infoTag " infoTags} \
@@ -480,6 +481,10 @@ task VcfStats {
             sep=" --sparkConfigValue" sparkConfigValues}
     }
 
+    output {
+        String resultsDir = outputDir
+    }
+
     runtime {
         cpu: localThreads
         memory: ceil(memory * memoryMultiplier)