Merge pull request #122 from biowdl/BIOWDL-297

Add feature type,idattr and additional attributes to htseq-count task.

CHANGELOG.md

@@ -11,4 +11,6 @@ that users understand how the changes affect the new version.
 
 version 1.0.0-dev
 ---------------------------
++ Add feature type, idattr and additional attributes to htseq-count.
 + Added allow-contain option to bowtie.
++ Added a changelog to keep track of changes.

htseq.wdl

@@ -9,6 +9,9 @@ task HTSeqCount {
         String format = "bam"
         String order = "pos"
         String stranded = "no"
+        String? featureType
+        String? idattr
+        Array[String] additionalAttributes = []
 
         Int memory = 40
         String dockerImage = "quay.io/biocontainers/htseq:0.9.1--py36h7eb728f_2"
@@ -21,6 +24,9 @@ task HTSeqCount {
         -f ~{format} \
         -r ~{order} \
         -s ~{stranded} \
+        ~{"--type " + featureType} \
+        ~{"--idattr " + idattr} \
+        ~{true="--additional-attr " false="" length(additionalAttributes) > 0 }~{sep=" --additional-attr " additionalAttributes} \
         ~{sep=" " inputBams} \
         ~{gtfFile} \
         > ~{outputTable}