From 91a6841a4f1280114da9e86c0cabe6be35360a33 Mon Sep 17 00:00:00 2001
From: npappas <N.Pappas@lumc.nl>
Date: Tue, 8 May 2018 13:18:26 +0200
Subject: [PATCH] Flash task
---
flash.wdl | 57 +++++++++++++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 57 insertions(+)
create mode 100644 flash.wdl
diff --git a/flash.wdl b/flash.wdl
new file mode 100644
index 0000000..0cabd06
--- /dev/null
+++ b/flash.wdl
@@ -0,0 +1,57 @@
+#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])
+ }
+
+}
\ No newline at end of file
--
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