Merge pull request #264 from biowdl/hs-metrics

Add parameter meta

picard.wdl

@@ -122,8 +122,10 @@ task CollectHsMetrics {
         referenceFastaDict: {description: "The sequence dictionary associated with the reference fasta file.", category: "required"}
         referenceFastaFai: {description: "The index for the reference fasta file.", category: "required"}
         targets: {description: "Picard interval file of the capture targets.", category: "required"}
+        targetsFile: {description: "Picard interval file of the capture targets, the same as targets.", category: "advanced"}
         basename: {description: "The basename/prefix of the output files (may include directories).", category: "required"}
         baits: {description: "Picard interval file of the capture bait set.", category: "advanced"}
+        baitsFile: {description: "Picard interval file of the bait set. Uses targets as a fallback when baits is not set.", category: "advanced"}
         javaXmxMb: {description: "The maximum memory available to the program in megabytes. Should be lower than `memoryMb` to accommodate JVM overhead.", category: "advanced"}
         memoryMb: {description: "The amount of memory this job will use in megabytes.", category: "advanced"}
         timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}