From b31f4001c674c1b252c79eca791441adf69666e9 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Tue, 30 Jan 2018 13:46:26 +0100
Subject: [PATCH] add seqtk sample task
---
seqtk.wdl | 25 +++++++++++++++++++++++++
1 file changed, 25 insertions(+)
create mode 100644 seqtk.wdl
diff --git a/seqtk.wdl b/seqtk.wdl
new file mode 100644
index 0000000..935669c
--- /dev/null
+++ b/seqtk.wdl
@@ -0,0 +1,25 @@
+task sample {
+ File sequenceFile
+ File? outFilePath = "subsampledReads"
+ String? preCommand
+ Int? seed
+ Boolean? twoPassMode
+ Float? fraction
+ Int? number
+ Boolean? zip
+
+ command {
+ set -e -o pipefail
+ ${preCommand}
+ seqtk sample \
+ ${"-s " + seed} \
+ ${true="-2 " false="" twoPassMode} \
+ ${sequenceFile} \
+ ${number} ${fraction} \
+ ${true="| gzip" false="" zip} \
+ ${"> " + outFilePath}
+ }
+ output {
+ File subsampledReads=select_first([outFilePath])
+ }
+}
\ No newline at end of file
--
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