make outputs write to files and prefix is a must

biopet.wdl

@@ -85,7 +85,7 @@ task BaseCounter {
     File bam
     File refFlat
     String outputDir
-    String? prefix
+    String prefix
 
     command {
         set -e -o pipefail
@@ -95,7 +95,7 @@ task BaseCounter {
         -b ${bam} \
         -r ${refFlat} \
         -o ${outputDir} \
-        ${"-p" + prefix}
+        -p ${prefix}
     }
 
     output {

htseq.wdl

 task HTSeqCount {
+    String? preCommand
     Array[File] alignmentFiles
     File gffFile
-
+    String outputTable
     String? format
     String? order
     String? stranded
 
-    String? preCommand
-
     command {
         set -e -o pipefail
         ${preCommand}
@@ -16,10 +15,11 @@ task HTSeqCount {
         -r ${default="pos" order} \
         -s ${default="no" stranded} \
         ${sep=" " alignmentFiles} \
-        ${gffFile}
+        ${gffFile} \
+        > ${outputTable}
     }
 
     output {
-        File counts = stdout()
+        File counts = outputTable
     }
 }
\ No newline at end of file

stringtie.wdl

@@ -3,6 +3,7 @@ task Stringtie {
     File alignedReads
     File? referenceGFF
     Int? threads
+    String assembledTranscripts
 
     command {
         set -e -o pipefail
@@ -10,11 +11,12 @@ task Stringtie {
         stringtie \
         ${"-p " + threads} \
         ${"-G " + referenceGFF} \
-        ${alignedReads}
+        ${alignedReads} \
+        > ${assembledTranscripts}
     }
 
     output {
-        File assembledTranscripts = stdout()
+        File assembledTranscripts = assembledTranscripts
     }
 
     runtime {