Flash task

flash.wdl

+#workflow runFlash {
+#    String preCommand
+#    String outDirPath
+#    File R1
+#    File R2
+#
+#    call flash {
+#        input:
+#            preCommand = preCommand,
+#            outDirPath = outDirPath,
+#            inputR1 = R1,
+#            inputR2 = R2,
+#    }
+#}
+task flash {
+    String? preCommand
+    File inputR1
+    File inputR2
+    String outDirPath
+    String? outPrefix = "flash"
+    String? logPath = outDirPath + "/" + outPrefix + ".log"
+    Int? minOverlap
+    Int? maxOverlap
+    Boolean? compress = true
+    Int? threads = 1
+    Int? memory = 4
+    Int? cores = 1
+
+    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} 2>&1 | tee ${logPath}
+    }
+
+    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"
+        String log = select_first([logPath])
+    }
+
+    runtime {
+        cpu: select_first([cores])
+        memory: select_first([memory])
+    }
+
+}
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