From c0aef2ef788ddaf8a2752fa74c996045279274e3 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 9 Mar 2021 09:19:29 +0100
Subject: [PATCH] gatk4: change -nct to --spark-master option
---
src/nf_modules/gatk4/main.nf | 22 +++++++++++-----------
1 file changed, 11 insertions(+), 11 deletions(-)
diff --git a/src/nf_modules/gatk4/main.nf b/src/nf_modules/gatk4/main.nf
index f37f2808..97cd6138 100644
--- a/src/nf_modules/gatk4/main.nf
+++ b/src/nf_modules/gatk4/main.nf
@@ -16,7 +16,7 @@ process variant_calling {
xmx_memory = "${task.memory}" - ~/\s*GB/
"""
gatk --java-options "-Xmx${xmx_memory}G" HaplotypeCaller \
- -nct ${task.cpus} \
+ --spark-master local[${task.cpus}] \
-R ${fasta} \
-I ${bam} \
-o ${file_id}.vcf
@@ -37,7 +37,7 @@ process filter_snp {
xmx_memory = "${task.memory}" - ~/\s*GB/
"""
gatk --java-options "-Xmx${xmx_memory}G" SelectVariants \
- -nct ${task.cpus} \
+ --spark-master local[${task.cpus}] \
-R ${fasta} \
-V ${vcf} \
-selectType SNP \
@@ -59,7 +59,7 @@ process filter_indels {
xmx_memory = "${task.memory}" - ~/\s*GB/
"""
gatk --java-options "-Xmx${xmx_memory}G"-T SelectVariants \
- -nct ${task.cpus} \
+ --spark-master local[${task.cpus}] \
-R ${fasta} \
-V ${vcf} \
-selectType INDEL \
@@ -83,7 +83,7 @@ process high_confidence_snp {
xmx_memory = "${task.memory}" - ~/\s*GB/
"""
gatk --java-options "-Xmx${xmx_memory}G"-T VariantFiltration \
- -nct ${task.cpus} \
+ --spark-master local[${task.cpus}] \
-R ${fasta} \
-V ${vcf} \
--filterExpression "${high_confidence_snp_filter}" \
@@ -108,7 +108,7 @@ process high_confidence_indels {
xmx_memory = "${task.memory}" - ~/\s*GB/
"""
gatk --java-options "-Xmx${xmx_memory}G" VariantFiltration \
- -nct ${task.cpus} \
+ --spark-master local[${task.cpus}] \
-R ${fasta} \
-V ${vcf} \
--filterExpression "${high_confidence_indel_filter}" \
@@ -131,7 +131,7 @@ process recalibrate_snp_table {
xmx_memory = "${task.memory}" - ~/\s*GB/
"""
gatk --java-options "-Xmx${xmx_memory}G" BaseRecalibrator \
- -nct ${task.cpus} \
+ --spark-master local[${task.cpus}] \
-R ${fasta} \
-I ${bam} \
-knownSites ${snp_file} \
@@ -157,7 +157,7 @@ process recalibrate_snp {
gatk --java-options "-Xmx${xmx_memory}G" PrintReads \
--use_jdk_deflater \
--use_jdk_inflater \
- -nct ${task.cpus} \
+ --spark-master local[${task.cpus}] \
-R ${fasta} \
-I ${bam} \
-BQSR recal_data_table \
@@ -179,7 +179,7 @@ process haplotype_caller {
xmx_memory = "${task.memory}" - ~/\s*GB/
"""
gatk --java-options "-Xmx${xmx_memory}G" HaplotypeCaller \
- -nct ${task.cpus} \
+ --spark-master local[${task.cpus}] \
-R ${fasta} \
-I ${bam} \
-ERC GVCF \
@@ -202,7 +202,7 @@ process gvcf_genotyping {
xmx_memory = "${task.memory}" - ~/\s*GB/
"""
gatk --java-options "-Xmx${xmx_memory}G" GenotypeGVCFs \
- -nct ${task.cpus} \
+ --spark-master local[${task.cpus}] \
-R ${fasta} \
-V ${gvcf} \
-o ${file_id}_joint.vcf
@@ -223,7 +223,7 @@ process select_variants_snp {
xmx_memory = "${task.memory}" - ~/\s*GB/
"""
gatk --java-options "-Xmx${xmx_memory}GG" SelectVariants \
- -nct ${task.cpus} \
+ --spark-master local[${task.cpus}] \
-R ${fasta} \
-V ${vcf} \
-selectType SNP \
@@ -245,7 +245,7 @@ process select_variants_indels {
xmx_memory = "${task.memory}" - ~/\s*GB/
"""
gatk --java-options "-Xmx${xmx_memory}G" SelectVariants \
- -nct ${task.cpus} \
+ --spark-master local[${task.cpus}] \
-R ${fasta} \
-V ${vcf} \
-selectType INDEL \
--
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