From 2de465dcc7c3c07bca2b0c4512aeeb1a9f33b361 Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Tue, 9 Jul 2019 13:04:59 +0200
Subject: [PATCH] add task for chunked-scatter
---
chunked-scatter.wdl | 33 +++++++++++++++++++++++++++++++++
1 file changed, 33 insertions(+)
create mode 100644 chunked-scatter.wdl
diff --git a/chunked-scatter.wdl b/chunked-scatter.wdl
new file mode 100644
index 0000000..97affd2
--- /dev/null
+++ b/chunked-scatter.wdl
@@ -0,0 +1,33 @@
+version 1.0
+
+task ChunkedScatter {
+ input {
+ File inputFile
+ String prefix = "./scatter"
+ Int? chunkSize
+ Int? overlap
+ Int? minimumBasesPerFile
+
+ String dockerImage = "alpine:latest" #TODO
+ }
+
+ command {
+ set -e
+ mkdir -p ~{prefix}
+ chunked-scatter \
+ -p ~{prefix} \
+ -i ~{inputFile} \
+ ~{"-c " + chunkSize} \
+ ~{"-o " + overlap} \
+ ~{"-m " + minimumBasesPerFile}
+ }
+
+ output {
+ Array[File] scatters = glob(prefix + "_*.bed")
+ }
+
+ runtime {
+ memory: 4
+ docker: dockerImage
+ }
+}
\ No newline at end of file
--
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