From 803337815de5579b4f1078a7fc7d87c35bcd60b0 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Tue, 6 Mar 2018 10:03:12 +0100
Subject: [PATCH] add poretools fastq task
---
poretools.wdl | 33 +++++++++++++++++++++++++++++++++
1 file changed, 33 insertions(+)
create mode 100644 poretools.wdl
diff --git a/poretools.wdl b/poretools.wdl
new file mode 100644
index 0000000..5f96160
--- /dev/null
+++ b/poretools.wdl
@@ -0,0 +1,33 @@
+task fastq {
+ Array[File] files
+ String outputFile
+ String? preCommand
+ String? type
+ String? start
+ String? end
+ Int? minLength
+ Int? maxLength
+ Boolean? highQuality
+ Boolean? normalQuality
+ String? group
+ command {
+ set -e -o pipefail
+ mkdir -p $(dirname ${outputFile})
+ ${preCommand}
+
+ poretools fastq \
+ ${"--type " + type} \
+ ${"--start " + start } \
+ ${"--end " + end } \
+ ${"--min-length " + minLength } \
+ ${"--max-length " + maxLength } \
+ ${if highQuality then "--high-quality" else ""} \
+ ${if normalQuality then "--normal-quality" else ""} \
+ ${"--group " + group} \
+ ${sep=" " files} > ${outputFile}
+ }
+
+ output {
+ File fastq = outputFile
+ }
+}
\ No newline at end of file
--
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