From 5a961182360fbcaf304825628338a33e5839c18e Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 7 May 2018 11:58:32 +0200
Subject: [PATCH] add FastQsync
---
biopet.wdl | 27 +++++++++++++++++++++++++++
1 file changed, 27 insertions(+)
diff --git a/biopet.wdl b/biopet.wdl
index 054a166..e13d763 100644
--- a/biopet.wdl
+++ b/biopet.wdl
@@ -90,6 +90,33 @@ task FastqSplitter {
}
}
+task FastqSync {
+ String? preCommand
+ File ref1
+ File ref2
+ File in1
+ File in2
+ String out1path
+ String out2path
+ File tool_jar
+ command {
+ set -e -o pipefail
+ ${preCommand}
+ mkdir -p $(dirname ${out1path}) $(dirname ${out2path})
+ java -jar ${tool_jar} \
+ --in1 ${in1} \
+ --in2 ${in2} \
+ --ref1 ${ref1} \
+ --ref2 ${ref2} \
+ --out1 ${out1path} \
+ --out2 ${out2path}
+ }
+ output {
+ File out1 = out1path
+ File out2 = out2path
+ }
+}
+
task SampleConfig {
String? preCommand
String tool_jar
--
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