From b18b1efef2acd9a59ec71b3952c77da6e661e7be Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Tue, 9 Mar 2021 09:57:15 +0100
Subject: [PATCH] gatk4: remove spark...
---
src/nf_modules/gatk4/main.nf | 19 +++++++------------
1 file changed, 7 insertions(+), 12 deletions(-)
diff --git a/src/nf_modules/gatk4/main.nf b/src/nf_modules/gatk4/main.nf
index a92b0ee3..6a19e272 100644
--- a/src/nf_modules/gatk4/main.nf
+++ b/src/nf_modules/gatk4/main.nf
@@ -3,7 +3,7 @@ container_url = "broadinstitute/gatk:${version}"
process variant_calling {
container = "${container_url}"
- label "big_mem_multi_cpus"
+ label "big_mem_mono_cpus"
tag "$file_id"
input:
@@ -15,8 +15,7 @@ process variant_calling {
script:
xmx_memory = "${task.memory}" - ~/\s*GB/
"""
-gatk --java-options "-Xmx${xmx_memory}G" HaplotypeCallerSpark \
- --spark-master local[${task.cpus}] \
+gatk --java-options "-Xmx${xmx_memory}G" HaplotypeCaller \
-R ${fasta} \
-I ${bam} \
-O ${file_id}.vcf
@@ -25,7 +24,7 @@ gatk --java-options "-Xmx${xmx_memory}G" HaplotypeCallerSpark \
process filter_snp {
container = "${container_url}"
- label "big_mem_multi_cpus"
+ label "big_mem_mono_cpus"
tag "$file_id"
input:
@@ -115,7 +114,7 @@ gatk --java-options "-Xmx${xmx_memory}G" VariantFiltration \
process recalibrate_snp_table {
container = "${container_url}"
- label "big_mem_multi_cpus"
+ label "big_mem_mono_cpus"
tag "$file_id"
input:
@@ -126,8 +125,7 @@ process recalibrate_snp_table {
script:
xmx_memory = "${task.memory}" - ~/\s*GB/
"""
-gatk --java-options "-Xmx${xmx_memory}G" BaseRecalibratorSpark \
- --spark-master local[${task.cpus}] \
+gatk --java-options "-Xmx${xmx_memory}G" BaseRecalibrator \
-R ${fasta} \
-I ${bam} \
-knownSites ${snp_file} \
@@ -162,7 +160,7 @@ gatk --java-options "-Xmx${xmx_memory}G" PrintReads \
process haplotype_caller {
container = "${container_url}"
- label "big_mem_multi_cpus"
+ label "big_mem_mono_cpus"
tag "$file_id"
input:
@@ -173,8 +171,7 @@ process haplotype_caller {
script:
xmx_memory = "${task.memory}" - ~/\s*GB/
"""
-gatk --java-options "-Xmx${xmx_memory}G" HaplotypeCallerSpark \
- --spark-master local[${task.cpus}] \
+gatk --java-options "-Xmx${xmx_memory}G" HaplotypeCaller \
-R ${fasta} \
-I ${bam} \
-ERC GVCF \
@@ -217,7 +214,6 @@ process select_variants_snp {
xmx_memory = "${task.memory}" - ~/\s*GB/
"""
gatk --java-options "-Xmx${xmx_memory}GG" SelectVariants \
- --spark-master local[${task.cpus}] \
-R ${fasta} \
-V ${vcf} \
-selectType SNP \
@@ -239,7 +235,6 @@ process select_variants_indels {
xmx_memory = "${task.memory}" - ~/\s*GB/
"""
gatk --java-options "-Xmx${xmx_memory}G" SelectVariants \
- --spark-master local[${task.cpus}] \
-R ${fasta} \
-V ${vcf} \
-selectType INDEL \
--
GitLab