diff --git a/CHANGELOG.md b/CHANGELOG.md
index 22f4182626273068c3dc6f8faa1b3722574762ef..58d9f57f9a595ae93bb525bb3aa4f9b9963adcc4 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,8 @@ that users understand how the changes affect the new version.
 
 version 5.0.0-dev
 ---------------------------
++ GffCompare: Make the `referenceAnnotation` input optional.
++ Stringtie: Add the `minimumCoverage` input.
 + mergePacBio: Rename `mergedReport` to `outputPathMergedReport`.
 + Lima: Fix copy commands.
 + Fixed the `size` call in the default for gffread's timeMinutes, to retrieve
diff --git a/htseq.wdl b/htseq.wdl
index ef4ae0a3e071e5dc64445428b0827cf82f3e6667..76d3bb8369c624a3f8981f8afad0f73ae9f68d3e 100644
--- a/htseq.wdl
+++ b/htseq.wdl
@@ -23,7 +23,6 @@ version 1.0
 task HTSeqCount {
     input {
         Array[File]+ inputBams
-        Array[File]+ inputBamIndexes
         File gtfFile
         String outputTable = "output.tsv"
         String order = "pos"