add some missing inputs to gridss AnnotateInsertedSequence and add missing \ to bcftools Filter

bcftools.wdl

@@ -146,7 +146,7 @@ task Filter {
         filter \
         ~{"-i " + include} \
         ~{"-e " + exclude} \
-        ~{"-s " + softFilter}
+        ~{"-s " + softFilter} \
         ~{vcf} \
         -O z \
         -o ~{outputPath}

gridss.wdl

@@ -91,6 +91,8 @@ task AnnotateInsertedSequence {
         File inputVcf
         String outputPath = "gridss.annotated.vcf.gz"
         File viralReference
+        File viralReferenceFai
+        File viralReferenceDict
 
         Int threads = 8
         String javaXmx = "8G"