add featureType

htseq.wdl

@@ -9,6 +9,7 @@ task HTSeqCount {
         String format = "bam"
         String order = "pos"
         String stranded = "no"
+        String featureType
 
         Int memory = 40
         String dockerImage = "quay.io/biocontainers/htseq:0.9.1--py36h7eb728f_2"
@@ -21,6 +22,7 @@ task HTSeqCount {
         -f ~{format} \
         -r ~{order} \
         -s ~{stranded} \
+        --type ~{featureType} \
         ~{sep=" " inputBams} \
         ~{gtfFile} \
         > ~{outputTable}