From b0d40e660a29b63cd35e937a2147e02587a0840c Mon Sep 17 00:00:00 2001
From: DavyCats <davycats.dc@gmail.com>
Date: Wed, 4 Apr 2018 16:02:06 +0200
Subject: [PATCH] adjust memory
---
biopet.wdl | 4 ++--
fastqc.wdl | 2 +-
gatk.wdl | 7 +++++--
3 files changed, 8 insertions(+), 5 deletions(-)
diff --git a/biopet.wdl b/biopet.wdl
index 7271f63..d76a3cc 100644
--- a/biopet.wdl
+++ b/biopet.wdl
@@ -82,7 +82,7 @@ task SampleConfig {
}
runtime {
- memory: ceil(select_first([memory, 3.0]) * select_first([memoryMultiplier, 1.5]))
+ memory: ceil(select_first([memory, 3.0]) * select_first([memoryMultiplier, 2.0]))
}
}
@@ -146,6 +146,6 @@ task BaseCounter {
}
runtime {
- memory: ceil(select_first([memory, 12.0]) * select_first([memoryMultiplier, 1.5]))
+ memory: ceil(select_first([memory, 12.0]) * select_first([memoryMultiplier, 2.0]))
}
}
diff --git a/fastqc.wdl b/fastqc.wdl
index d7850ac..e526c1e 100644
--- a/fastqc.wdl
+++ b/fastqc.wdl
@@ -89,7 +89,7 @@ task extractAdapters {
}
runtime {
- memory: ceil(select_first([memory, 4.0]) * select_first([memoryMultiplier, 1.5]))
+ memory: ceil(select_first([memory, 4.0]) * select_first([memoryMultiplier, 2.0]))
}
}
diff --git a/gatk.wdl b/gatk.wdl
index 6edac93..6d05711 100644
--- a/gatk.wdl
+++ b/gatk.wdl
@@ -12,10 +12,13 @@ task BaseRecalibrator {
File ref_fasta
File ref_fasta_index
+ Float? memory
+ Float? memoryMultiplier
+
command {
set -e -o pipefail
${preCommand}
- java -Xms4G -jar ${gatk_jar} \
+ java -Xms${true=memory false="4" defined(memory)}G -jar ${gatk_jar} \
BaseRecalibrator \
-R ${ref_fasta} \
-I ${input_bam} \
@@ -30,7 +33,7 @@ task BaseRecalibrator {
}
runtime {
- memory: 6
+ memory: ceil(select_first([memory, 4.0]) * select_first([memoryMultiplier, 2]))
}
}
--
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