bugfixes'

bwa.wdl

@@ -81,7 +81,7 @@ task mem {
         ${referenceFile} ${read1} ${read2}
     }
     output {
-        File samFile = if defined(outputFile) then outputFile else stdout()
+        File samFile = if defined(outputFile) then select_first([outputFile]) else stdout()
     }
     runtime {
         cpu: select_first([threads])

spades.wdl

@@ -63,7 +63,7 @@ task spades {
         ${"--phred-offset " + phredOffset }
     }
     output {
-        Array[File] correctedReads = glob_wildcard(outputDir + "/corrected/*.fastq*")
+        Array[File] correctedReads = glob(outputDir + "/corrected/*.fastq*")
         File scaffolds = outputDir + "/scaffolds.fasta"
         File contigs = outputDir + "/contigs.fasta"
         File assemblyGraphGfa = outputDir + "/assembly_graph.gfa"