Merge pull request #12 from biowdl/flash

Adding flash task for combining overlapping reads

flash.wdl

+task flash {
+    String? preCommand
+    File inputR1
+    File inputR2
+    String outdirPath
+    String? outPrefix = "flash"
+    Int? minOverlap
+    Int? maxOverlap
+    Boolean? compress = true
+    Int? threads
+    Int? memory
+
+    command {
+        set -e -o pipefail
+        mkdir -p ${outdirPath}
+        ${preCommand}
+        flash \
+        ${"--threads=" + threads} \
+        ${"--output-directory=" + outdirPath} \
+        ${"--output-prefix=" + outPrefix} \
+        ${true="--compress " false="" defined(compress)} \
+        ${"--min-overlap=" + minOverlap} \
+        ${"--max-overlap=" + maxOverlap} \
+        ${inputR1} ${inputR2}
+    }
+
+    output {
+        File extendedFrags = outdirPath + "/" + outPrefix + ".extendedFrags.fastq.gz"
+        File notCombined1 = outdirPath + "/" + outPrefix + ".notCombined_1.fastq.gz"
+        File notCombined2 = outdirPath + "/" + outPrefix + ".notCombined_2.fastq.gz"
+        File hist = outdirPath + "/" + outPrefix + ".hist"
+        File histogram = outdirPath + "/" + outPrefix + ".histogram"
+    }
+
+    runtime {
+        cpu: select_first([threads, 2])
+        memory: select_first([memory, 2])
+    }
+
+}
\ No newline at end of file