From d05ae22db47d5b9094734cec7eb6cfb8441ebfd1 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 20 Aug 2018 12:59:21 +0200
Subject: [PATCH] Switch to new tool
---
biopet.wdl | 33 +++++++++++++++++++++++++++++++++
1 file changed, 33 insertions(+)
diff --git a/biopet.wdl b/biopet.wdl
index a3ecdd0..a7cd28b 100644
--- a/biopet.wdl
+++ b/biopet.wdl
@@ -244,6 +244,39 @@ task SampleConfig {
}
}
+task SampleConfigCromwellArrays {
+ input {
+ File? toolJar
+ String? preCommand
+ Array[File]+ inputFiles
+ String outputPath
+
+ Int memory = 4
+ Float memoryMultiplier = 2.0
+ }
+
+ String toolCommand = if defined(toolJar)
+ then "java -Xmx" + memory + "G -jar " +toolJar
+ else "biopet-sampleconfig -Xmx" + memory + "G"
+
+ command {
+ set -e -o pipefail
+ ~{preCommand}
+ mkdir -p . ~{"$(dirname " + outputPath + ")"}
+ ~{toolCommand} CromwellArrays \
+ -i ~{sep="-i " inputFiles} \
+ ~{"-o " + outputPath}
+ }
+
+ output {
+ File outputFile = outputPath
+ }
+
+ runtime {
+ memory: ceil(memory * memoryMultiplier)
+ }
+}
+
task ScatterRegions {
input {
String? preCommand
--
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