rename gff to gtf

htseq.wdl

 task HTSeqCount {
     String? preCommand
     Array[File] alignmentFiles
-    File gffFile
+    File gtfFile
     String outputTable
     String? format
     String? order
@@ -17,7 +17,7 @@ task HTSeqCount {
         -r ${default="pos" order} \
         -s ${default="no" stranded} \
         ${sep=" " alignmentFiles} \
-        ${gffFile} \
+        ${gtfFile} \
         > ${outputTable}
     }
 

stringtie.wdl

 task Stringtie {
     String? preCommand
     File alignedReads
-    File? referenceGFF
+    File? referenceGtf
     Int? threads
     String assembledTranscriptsFile
     Boolean? firstStranded
@@ -13,7 +13,7 @@ task Stringtie {
         ${preCommand}
         stringtie \
         ${"-p " + threads} \
-        ${"-G " + referenceGFF} \
+        ${"-G " + referenceGtf} \
         ${true="--rf" false="" firstStranded} \
         ${true="fr" false="" secondStranded} \
         -o ${assembledTranscriptsFile} \