From 40852ab167a7705814c41cd2aa1e5513e05fdec8 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 14 May 2018 12:48:18 +0200
Subject: [PATCH] add runtime section for samtools view
---
samtools.wdl | 5 +++++
1 file changed, 5 insertions(+)
diff --git a/samtools.wdl b/samtools.wdl
index 5bb6d09..59f5b0e 100644
--- a/samtools.wdl
+++ b/samtools.wdl
@@ -129,6 +129,7 @@ task view {
Int? excludeFilter
Int? excludeSpecificFilter
Int? threads
+ Int? memory
command {
set -e -o pipefail
@@ -148,4 +149,8 @@ task view {
output {
File outputFile = outputFileName
}
+ runtime {
+ cpu: select_first([threads, 1])
+ memory: select_first([memory, 1])
+ }
}
--
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