From dd9990d9737b5c75e125d0171af9ea3718e2b745 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 14 May 2018 16:41:19 +0200
Subject: [PATCH] fix spades memory allocation
---
spades.wdl | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/spades.wdl b/spades.wdl
index ce9de29..7fd0c98 100644
--- a/spades.wdl
+++ b/spades.wdl
@@ -28,8 +28,8 @@ task spades {
Float? covCutoff
Int? phredOffset
Int finalThreads = select_first([threads,1])
- Int totalMemory = select_first([memoryGb, finalThreads * 16])
- Int clusterMemory = totalMemory / finalThreads
+ Float totalMemory = select_first([memoryGb, finalThreads * 16])
+ Int clusterMemory = ceil(totalMemory / finalThreads)
command {
set -e -o pipefail
@@ -57,7 +57,7 @@ task spades {
${true="--disable-rr" false="" disableRepeatResolution } \
${"--dataset " + dataset } \
${"--threads " + finalThreads} \
- ${"--memory " + totalMemory } \
+ ${"--memory " + ceil(totalMemory) } \
${"-k " + k } \
${"--cov-cutoff " + covCutoff } \
${"--phred-offset " + phredOffset }
--
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