From a4af699b14f325e1729e307a21058cb25da0d251 Mon Sep 17 00:00:00 2001
From: cagaser <c.agaser@lumc.nl>
Date: Thu, 13 Aug 2020 15:06:02 +0200
Subject: [PATCH] update gridss: add --jvmheap parameter
---
gridss.wdl | 2 ++
1 file changed, 2 insertions(+)
diff --git a/gridss.wdl b/gridss.wdl
index 3d4b7d7..4ba4bc1 100644
--- a/gridss.wdl
+++ b/gridss.wdl
@@ -33,6 +33,7 @@ task GRIDSS {
BwaIndex reference
String outputPrefix = "gridss"
+ String jvmheapsize = "25G"
Int threads = 1
String dockerImage = "quay.io/biocontainers/gridss:2.9.4--0"
}
@@ -45,6 +46,7 @@ task GRIDSS {
--output ~{outputPrefix}.vcf.gz \
--assembly ~{outputPrefix}_assembly.bam \
~{"-t " + threads} \
+ ~{"--jvmheap " + jvmheapsize} \
--label ~{normalLabel}~{true="," false="" defined(normalLabel)}~{tumorLabel} \
~{normalBam} \
~{tumorBam}
--
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