From 4a94020d18885fa28ba7e1831d7a4bca64b14a30 Mon Sep 17 00:00:00 2001
From: Redmar van den Berg <RedmarvandenBerg@lumc.nl>
Date: Wed, 14 Jul 2021 10:03:03 +0200
Subject: [PATCH] Set java temp dir for picard markduplicates
---
Snakefile | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/Snakefile b/Snakefile
index 9c0bcbf..ac63adc 100644
--- a/Snakefile
+++ b/Snakefile
@@ -302,7 +302,7 @@ rule markdup:
bai = "{sample}/bams/{sample}.markdup.bai",
metrics = "{sample}/bams/{sample}.markdup.metrics"
singularity: "docker://quay.io/biocontainers/picard:2.14--py36_0"
- shell: "picard -Xmx4G MarkDuplicates CREATE_INDEX=TRUE TMP_DIR={input.tmp} "
+ shell: "picard -Xmx4G -Djava.io.tmpdir={input.tmp} MarkDuplicates CREATE_INDEX=TRUE TMP_DIR={input.tmp} "
"INPUT={input.bam} OUTPUT={output.bam} "
"METRICS_FILE={output.metrics} "
"MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=500"
--
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