make intervals optional, allow exclude intervals

gatk.wdl

@@ -207,7 +207,8 @@ task HaplotypeCallerGvcf {
     input {
         Array[File]+ inputBams
         Array[File]+ inputBamsIndex
-        Array[File]+ intervalList
+        Array[File]+? intervalList
+        Array[File]+? excludeIntervalList
         String gvcfPath
         File referenceFasta
         File referenceFastaIndex
@@ -229,7 +230,8 @@ task HaplotypeCallerGvcf {
         -R ~{referenceFasta} \
         -O ~{gvcfPath} \
         -I ~{sep=" -I " inputBams} \
-        -L ~{sep=' -L ' intervalList} \
+        ~{true="-L" false="" defined(intervalList)} ~{sep=' -L ' intervalList} \
+        ~{true="-XL" false="" defined(excludeIntervalList)} ~{sep=' -XL ' excludeIntervalList} \
         ~{true="-D" false="" defined(dbsnpVCF)} ~{dbsnpVCF} \
         -contamination ~{contamination} \
         -ERC GVCF