From eebec9e48abc211e3dc748331a7c858b2df33645 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Fri, 9 Mar 2018 17:33:27 +0100
Subject: [PATCH] start on unicycler
---
unicycler.wdl | 30 ++++++++++++++++++++++++++++++
1 file changed, 30 insertions(+)
create mode 100644 unicycler.wdl
diff --git a/unicycler.wdl b/unicycler.wdl
new file mode 100644
index 0000000..dac7899
--- /dev/null
+++ b/unicycler.wdl
@@ -0,0 +1,30 @@
+task unicycler {
+ String? preCommand
+ File short1
+ File short2
+ File? unpaired
+ File? long
+ String out
+ Int? minFastaLength
+ Int? keep
+ Boolean? vcf
+ Int? threads = 1
+ Int? memory = 4
+ String? mode
+ Int? linearSeqs
+ Int? verbosity
+ command {
+ set -e -o pipefail
+ mkdir -p ${out}
+ ${preCommand}
+ unicycler \
+ --short1 ${short1}
+ --short2 ${short2}
+
+ }
+
+ runtime {
+ cpu: select_first([threads])
+ memory: select_first([memory])
+ }
+}
\ No newline at end of file
--
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