From ac34c1f878f76f7bd837ab9dc76956f587c0b9d6 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Fri, 19 Jan 2018 15:19:00 +0100
Subject: [PATCH] added extractAdapters task
---
fastqc.wdl | 28 ++++++++++++++++++++++++++++
1 file changed, 28 insertions(+)
diff --git a/fastqc.wdl b/fastqc.wdl
index 2b4cd87..65b9509 100644
--- a/fastqc.wdl
+++ b/fastqc.wdl
@@ -58,3 +58,31 @@ task fastqc {
cpu: select_first(threads)
}
}
+
+task extractAdapters {
+ File extractAdaptersFastqcJar
+ File inputFile
+ String? adapterOutputFilePath
+ String? contamsOutputFilePath
+ Boolean? skipContams
+ File? knownContamFile
+ File? knownAdapterFile
+ Float? adapterCutoff
+ Boolean? outputAsFasta
+ command {
+ java -jar ${extractAdaptersFastqcJar} \
+ --inputFile ${inputFile} \
+ ${"--adapterOutputFile " + adapterOutputFilePath } \
+ ${"--contamsOutputFile " + contamsOutputFilePath } \
+ ${"--knownContamFile " + knownContamFile} \
+ ${"--knownAdapterFile " + knownAdapterFile} \
+ ${"--adapterCutoff " + adapterCutoff} \
+ ${true="--skipContams" false="" skipContams} \
+ ${true="--outputAsFasta" false="" outputAsFasta}
+ }
+
+ output {
+ File? adapterOutputFile = adapterOutputFilePath
+ File? contamsOutputFile = contamsOutputFilePath
+ }
+}
\ No newline at end of file
--
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