Merge branch 'BIOWDL-85' of https://github.com/biowdl/tasks into BIOWDL-85

flash.wdl

 version 1.0
 
+import "common.wdl" as common
+
 task Flash {
     input {
         String? preCommand
-        File inputR1
-        File inputR2
+        FastqPair inputFastq
         String outdirPath
         String outPrefix = "flash"
         Int? minOverlap
@@ -25,13 +26,17 @@ task Flash {
         ~{true="--compress " false="" compress} \
         ~{"--min-overlap=" + minOverlap} \
         ~{"--max-overlap=" + maxOverlap} \
-        ~{inputR1} ~{inputR2}
+        ~{inputFastq.R1} ~{inputFastq.R2}
     }
 
     output {
         File extendedFrags = outdirPath + "/" + outPrefix + ".extendedFrags.fastq.gz"
         File notCombined1 = outdirPath + "/" + outPrefix + ".notCombined_1.fastq.gz"
         File notCombined2 = outdirPath + "/" + outPrefix + ".notCombined_2.fastq.gz"
+        FastqPair notCombined = object {
+          R1: notCombined1,
+          R2: notCombined2
+        }
         File hist = outdirPath + "/" + outPrefix + ".hist"
         File histogram = outdirPath + "/" + outPrefix + ".histogram"
     }