diff --git a/isoseq3.wdl b/isoseq3.wdl
index 604a71d50fa673b5d248b7edfc943ccc66150c82..7894b382000b96e9c876c5daf340c1546943a86c 100644
--- a/isoseq3.wdl
+++ b/isoseq3.wdl
@@ -26,6 +26,7 @@ task Refine {
         Boolean requirePolyA = false
         String logLevel = "WARN"
         File inputBamFile
+        File inputBamIndex
         File primerFile
         String outputDir
         String outputNamePrefix