From 8818f78d9a2652396fe6ac3a712924077cc03070 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Mon, 8 Mar 2021 10:43:27 +0100
Subject: [PATCH] gatk4: change Xmx option parsing
---
src/nf_modules/gatk4/main.nf | 12 +++++++-----
1 file changed, 7 insertions(+), 5 deletions(-)
diff --git a/src/nf_modules/gatk4/main.nf b/src/nf_modules/gatk4/main.nf
index 0b419ecd..e616741f 100644
--- a/src/nf_modules/gatk4/main.nf
+++ b/src/nf_modules/gatk4/main.nf
@@ -211,8 +211,9 @@ process select_variants_snp {
output:
tuple val(file_id), path("*_joint_snp.vcf"), emit: vcf
script:
+ xmx_memory = task.memory - ~/\s*GB/
"""
-gatk --java-options "-Xmx${task.memory}" -T SelectVariants \
+gatk --java-options "-Xmx${xmx_memory}G" -T SelectVariants \
-nct ${task.cpus} \
-R ${fasta} \
-V ${vcf} \
@@ -232,8 +233,9 @@ process select_variants_indels {
output:
tuple val(file_id), path("*_joint_indel.vcf"), emit: vcf
script:
+ xmx_memory = task.memory - ~/\s*GB/
"""
-gatk --java-options "-Xmx${task.memory}" -T SelectVariants \
+gatk --java-options "-Xmx${xmx_memory}" -T SelectVariants \
-nct ${task.cpus} \
-R ${fasta} \
-V ${vcf} \
@@ -254,12 +256,12 @@ process personalized_genome {
tuple val(file_id), path("*_genome.fasta"), emit: fasta
script:
- library = pick_library(file_id, library_list)
+ xmx_memory = task.memory - ~/\s*GB/
"""
-gatk --java-options "-Xmx${task.memory}" -T FastaAlternateReferenceMaker\
+gatk --java-options "-Xmx${xmx_memory}" -T FastaAlternateReferenceMaker\
-R ${reference} \
-V ${vcf} \
- -o ${library}_genome.fasta
+ -o ${file_id.library}_genome.fasta
"""
}
--
GitLab