stringtie to 1.0

stringtie.wdl

+version 1.0
+
 task Stringtie {
-    String? preCommand
-    File alignedReads
-    File? referenceGtf
-    Int? threads
-    String assembledTranscriptsFile
-    Boolean? firstStranded
-    Boolean? secondStranded
-    String? geneAbundanceFile
+    input {
+        String? preCommand
+        File alignedReads
+        File? referenceGtf
+        Int? threads
+        String assembledTranscriptsFile
+        Boolean? firstStranded
+        Boolean? secondStranded
+        String? geneAbundanceFile
+    }
 
     command {
         set -e -o pipefail
-        mkdir -p $(dirname ${assembledTranscriptsFile})
-        ${preCommand}
+        mkdir -p $(dirname ~{assembledTranscriptsFile})
+        ~{preCommand}
         stringtie \
-        ${"-p " + threads} \
-        ${"-G " + referenceGtf} \
-        ${true="--rf" false="" firstStranded} \
-        ${true="fr" false="" secondStranded} \
-        -o ${assembledTranscriptsFile} \
-        ${"-A " + geneAbundanceFile} \
-        ${alignedReads} \
+        ~{"-p " + threads} \
+        ~{"-G " + referenceGtf} \
+        ~{true="--rf" false="" firstStranded} \
+        ~{true="fr" false="" secondStranded} \
+        -o ~{assembledTranscriptsFile} \
+        ~{"-A " + geneAbundanceFile} \
+        ~{alignedReads} \
 
     }