diff --git a/bcftools.wdl b/bcftools.wdl
index 4703580a1e9691b7f74a4b8741b44446e383b0ca..d358ab7bac3bcda532e20346d6a7329c633f98a6 100644
--- a/bcftools.wdl
+++ b/bcftools.wdl
@@ -44,6 +44,7 @@ task Annotate {
         Boolean singleOverlaps = false
         Array[String] removeAnns = []
         File inputFile
+        File? inputFileIndex
         String outputPath = "output.vcf.gz"
         
         Int threads = 0
@@ -117,6 +118,7 @@ task Annotate {
         singleOverlaps: {description: "keep memory requirements low with very large annotation files.", category: "advanced"}
         removeAnns: {description: "List of annotations to remove (see man page for details).", category: "advanced"}
         inputFile: {description: "A vcf or bcf file.", category: "required"}
+        ipnutFileIndex: {description: "The index for the input vcf or bcf.", "common"}
 
         threads: {description: "Number of extra decompression threads [0].", category: "advanced"}
         dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.", category: "advanced"}
diff --git a/gridss.wdl b/gridss.wdl
index cfbb7069dc8c893179f077864ae623094eca31e4..c444c8545eb6866b45cd86c129b79291fecee1cb 100644
--- a/gridss.wdl
+++ b/gridss.wdl
@@ -93,6 +93,7 @@ task AnnotateInsertedSequence {
         File viralReference
         File viralReferenceFai
         File viralReferenceDict
+        File viralReferenceImg
 
         Int threads = 8
         String javaXmx = "8G"
@@ -134,6 +135,9 @@ task AnnotateInsertedSequence {
         inputVcf: {description: "The input VCF file.", category: "required"}
         outputPath: {description: "The path the output will be written to.", category: "common"}
         viralReference: {description: "A fasta file with viral sequences.", category: "required"}
+        viralReferenceFai: {description: "The index for the viral reference fasta.", category: "required"}
+        viralReferenceDict: {description: "The dict file for the viral reference.", category: "required"}
+        viralReferenceImg: {description: "The BWA index image (generated with GATK BwaMemIndexImageCreator) of the viral reference.", category: "required"}
 
         memory: {description: "The amount of memory this job will use.", category: "advanced"}
         javaXmx: {description: "The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.",
diff --git a/snpeff.wdl b/snpeff.wdl
index a26fadbd57c426c996d60805996528ac4029afd3..2a113c5258a2e3083b95153a93e5cb5d6f50ea99 100644
--- a/snpeff.wdl
+++ b/snpeff.wdl
@@ -1,5 +1,27 @@
 version 1.0
 
+# MIT License
+#
+# Copyright (c) 2020 Leiden University Medical Center
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
 task SnpEff {
     input {
         File vcf