diff --git a/somaticseq.wdl b/somaticseq.wdl
index 6164e64e44cddab537ec0ec63a7d215677d712fd..d1163b4a1fcda41b45f9e3a12e7eb5b2ad16c882 100644
--- a/somaticseq.wdl
+++ b/somaticseq.wdl
@@ -8,6 +8,7 @@ task ParallelPaired {
         File? classifierIndel
         String outputDir
         File referenceFasta
+        File referenceFastaFai
         File? inclusionRegion
         File? exclusionRegion
         File tumorBam
@@ -82,6 +83,7 @@ task ParallelPairedTrain {
         File truthIndel
         String outputDir
         File referenceFasta
+        File referenceFastaFai
         File? inclusionRegion
         File? exclusionRegion
         File tumorBam
@@ -155,6 +157,7 @@ task ParallelSingle {
         File? classifierIndel
         String outputDir
         File referenceFasta
+        File referenceFastaFai
         File? inclusionRegion
         File? exclusionRegion
         File bam
@@ -214,6 +217,7 @@ task ParallelSingleTrain {
         File truthIndel
         String outputDir
         File referenceFasta
+        File referenceFastaFai
         File? inclusionRegion
         File? exclusionRegion
         File bam