Merge branch 'develop' into SASC-844

star.wdl

@@ -15,9 +15,12 @@ task Star {
         String? outStd
         String? twopassMode
         Array[String]? outSAMattrRGline
+        String? outSAMunmapped = "Within KeepPairs"
         Int? limitBAMsortRAM
 
+
         Int memory = 48
+
     }
 
     # Needs to be extended for all possible output extensions
@@ -33,6 +36,7 @@ task Star {
         --genomeDir ~{genomeDir} \
         --outSAMtype ~{outSAMtype} \
         --readFilesCommand ~{readFilesCommand} \
+        ~{"--outSAMunmapped " + outSAMunmapped} \
         ~{"--runThreadN " + runThreadN} \
         ~{"--outStd " + outStd} \
         ~{"--twopassMode " + twopassMode} \