From 424178d62f31a773700f5e7fb46476fd043ab51e Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Mon, 22 Jun 2020 13:25:55 +0200
Subject: [PATCH] use correct memory estimate
---
bwa.wdl | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/bwa.wdl b/bwa.wdl
index 14b9a00..3f1276d 100644
--- a/bwa.wdl
+++ b/bwa.wdl
@@ -92,7 +92,7 @@ task Kit {
Boolean sixtyFour = false
Int threads = 4
- String memory = 1 + ceil(size(bwaIndex.indexFiles, "G"))
+ String memoryGb = 1 + ceil(size(bwaIndex.indexFiles, "G"))
Int timeMinutes = 1 + ceil(size([read1, read2], "G") * 220 / threads)
String dockerImage = "biocontainers/bwakit:v0.7.15_cv1"
}
@@ -121,7 +121,7 @@ task Kit {
# One extra thread for bwa-postalt + samtools is not needed.
# These only use 5-10% of compute power and not always simultaneously.
cpu: threads
- memory: memory
+ memory: "~{memoryGb}G"
time_minutes: timeMinutes
docker: dockerImage
}
@@ -136,7 +136,7 @@ task Kit {
sixtyFour: {description: "Whether or not the index uses the '.64' suffixes.", category: "common"}
threads: {description: "The number of threads to use for alignment.", category: "advanced"}
- memory: {description: "The amount of memory this job will use.", category: "advanced"}
+ memoryGb: {description: "The amount of memory this job will use in gigabytes.", category: "advanced"}
timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}
dockerImage: {description: "The docker image used for this task. Changing this may result in errors which the developers may choose not to address.",
category: "advanced"}
--
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