small fixes

collect-columns.wdl

@@ -13,7 +13,7 @@ task CollectColumns {
         File? referenceGtf
         String? featureAttribute
 
-        String dockerTag = "0.1.1--py_0"
+        String dockerTag = "0.2.0--py_1"
     }
 
     command {

mergecounts.wdl

 version 1.0
 
+#DEPRECATED
 task MergeCounts {
     input {
         Array[File] inputFiles

star.wdl

@@ -9,7 +9,7 @@ task Star {
         String outSAMtype = "BAM SortedByCoordinate"
         String readFilesCommand = "zcat"
         String? outStd
-        String? twopassMode
+        String? twopassMode = "Basic"
         Array[String]? outSAMattrRGline
         String? outSAMunmapped = "Within KeepPairs"
         Int? limitBAMsortRAM
@@ -19,7 +19,7 @@ task Star {
         String dockerTag = "2.6.0c--0"
     }
 
-    # Needs to be extended for all possible output extensions
+    #TODO Needs to be extended for all possible output extensions
     Map[String, String] samOutputNames = {"BAM SortedByCoordinate": "sortedByCoord.out.bam"}
 
     command {