From 58682093853cf6e62304d7797f3f268587187669 Mon Sep 17 00:00:00 2001
From: Ruben Vorderman <r.h.p.vorderman@lumc.nl>
Date: Tue, 18 Jan 2022 15:42:12 +0100
Subject: [PATCH] Have more records in ram
---
picard.wdl | 2 ++
1 file changed, 2 insertions(+)
diff --git a/picard.wdl b/picard.wdl
index 144c778..e81cd4e 100644
--- a/picard.wdl
+++ b/picard.wdl
@@ -1038,6 +1038,7 @@ task UmiAwareMarkDuplicatesWithMateCigar {
String outputPath
String outputPathMetrics = outputPath + ".metrics"
String outputPathUmiMetrics = outputPath + ".umi-metrics"
+ Int maxRecordsInRam = 3000000 # Default is 500_000 but that will lead to very small files on disk.
String? assumeSortOrder
String tempdir = "temp"
Boolean removeDuplicates = true
@@ -1063,6 +1064,7 @@ task UmiAwareMarkDuplicatesWithMateCigar {
UMI_METRICS_FILE=~{outputPathUmiMetrics} \
TMP_DIR=~{tempdir} \
REMOVE_DUPLICATES=~{removeDuplicates} \
+ MAX_RECORDS_IN_RAM=~{maxRecordsInRam} \
CREATE_INDEX=true \
COMPRESSION_LEVEL=~{compressionLevel} \
USE_JDK_INFLATER=~{true="true" false="false" useJdkInflater} \
--
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