some additions

picard.wdl

@@ -221,7 +221,7 @@ task GatherVcfs {
     input {
         Array[File]+ inputVcfs
         Array[File]+ inputVcfIndexes
-        String outputVcfPath
+        String outputVcfPath = "out.vcf.gz"
 
         Int memory = 4
         Float memoryMultiplier = 3.0
@@ -230,6 +230,7 @@ task GatherVcfs {
 
     command {
         set -e
+        mkdir -p $(dirname ~{outputVcfPath})
         picard -Xmx~{memory}G \
         GatherVcfs \
         INPUT=~{sep=' INPUT=' inputVcfs} \

samtools.wdl

@@ -64,7 +64,7 @@ task Merge {
 
     command {
         set -e
-        mkdir -p ~{outputBamPath}
+        mkdir -p $(dirname ~{outputBamPath})
         samtools merge ~{true="-f" false="" force} ~{outputBamPath} ~{sep=' ' bamFiles}
     }