fix seqstats

biopet/seqstat.wdl

+version 1.0
+
+# Copyright Sequencing Analysis Support Core - Leiden University Medical Center 2018
+
 task Generate {
     input {
         String? preCommand
         File? toolJar
         File fastqR1
-        File fastqR2
+        File? fastqR2
         String outputFile
-        String? sample
-        String? library
-        String? readgroup
+        String sample = "sample"
+        String library = "library"
+        String readgroup = "readgroup"
 
         Int memory = 4
         Float memoryMultiplier = 2.0
@@ -21,9 +25,9 @@ task Generate {
         set -e -o pipefail
         ~{preCommand}
         mkdir -p $(dirname ~{outputFile})
-        ~{toolCommand} \
+        ~{toolCommand} Generate \
         --fastqR1 ~{fastqR1} \
-        --fastqR2 ~{fastqR2} \
+        ~{"--fastqR2 " + fastqR2} \
         --output ~{outputFile} \
         ~{"--sample " + sample} \
         ~{"--library " + library } \