remove structs

vardict.wdl

@@ -5,10 +5,12 @@ import "common.wdl"
 task VarDict {
     input {
         String tumorSampleName
-        IndexedBamFile tumorBam
+        File tumorBam
+        File tumorBamIndex
         String? normalSampleName
-        IndexedBamFile? normalBam
-        Reference reference
+        File? normalBam
+        File? normalBamIndex
+        File referenceFasta
         File bedFile
         String outputVcf
 
@@ -22,21 +24,16 @@ task VarDict {
         Float memoryMultiplier = 2.5
         String dockerImage = "quay.io/biocontainers/vardict-java:1.5.8--1"
 
-        File? doNotDefineThis #FIXME
     }
 
-    File? normalBamFile = if defined(normalBam)
-        then select_first([normalBam]).file
-        else doNotDefineThis
-
     command {
         set -e -o pipefail
         export JAVA_OPTS="-Xmx~{memory}G"
         vardict-java \
         ~{"-th " + threads} \
-        -G ~{reference.fasta} \
+        -G ~{referenceFasta} \
         -N ~{tumorSampleName} \
-        -b "~{tumorBam.file}~{"|" + normalBamFile}" \
+        -b "~{tumorBam}~{"|" + normalBam}" \
         ~{true="" false="-z" defined(normalBam)} \
         -c ~{chromosomeColumn} \
         -S ~{startColumn} \