update changelog

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

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"