From 4402a95dc00cce75fffc55bb8bfec634425b42d8 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Wed, 17 Jun 2020 08:59:17 +0200
Subject: [PATCH] Update image and tasks for chunk scatter
---
chunked-scatter.wdl | 17 +++++++++--------
1 file changed, 9 insertions(+), 8 deletions(-)
diff --git a/chunked-scatter.wdl b/chunked-scatter.wdl
index 96dbf1e..6f2b465 100644
--- a/chunked-scatter.wdl
+++ b/chunked-scatter.wdl
@@ -28,27 +28,28 @@ task ChunkedScatter {
Int? overlap
Int? minimumBasesPerFile
+ String memory = "256M"
Int timeMinutes = 2
- String dockerImage = "quay.io/biocontainers/chunked-scatter:0.1.0--py_0"
+ String dockerImage = "quay.io/biocontainers/chunked-scatter:0.2.0--py_0"
}
command {
- set -e
- mkdir -p ~{prefix}
chunked-scatter \
+ --print-paths \
-p ~{prefix} \
- -i ~{inputFile} \
~{"-c " + chunkSize} \
~{"-o " + overlap} \
- ~{"-m " + minimumBasesPerFile}
+ ~{"-m " + minimumBasesPerFile} \
+ ~{inputFile}
}
output {
- Array[File] scatters = glob(prefix + "*.bed")
+ Array[File] scatters = read_lines(stdout())
}
runtime {
- memory: "4G"
+ cpu: 1
+ memory: memory
time_minutes: timeMinutes
docker: dockerImage
}
@@ -75,7 +76,7 @@ task ScatterRegions {
Int? scatterSize
Int timeMinutes = 2
String memory = "256M"
- String dockerImage = "biowdl/chunked-scatter:latest"
+ String dockerImage = "quay.io/biocontainers/chunked-scatter:0.2.0--py_0"
}
String finalSize = if defined(scatterSize) then "~{scatterSize}" else "~{scatterSizeMillions}000000"
--
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