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Verified Commit 2d1951f6 authored by Laurent Modolo's avatar Laurent Modolo
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gatk4: try to fix task memory parsing

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src/nf_modules/gatk4/main.nf
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...@@ -13,7 +13,7 @@ process variant_calling { ...@@ -13,7 +13,7 @@ process variant_calling {
tuple val(file_id), path("*.vcf"), emit: vcf tuple val(file_id), path("*.vcf"), emit: vcf
script: script:
xmx_memory = task.memory - ~/\s*GB/ xmx_memory = "${task.memory}" - ~/\s*GB/
""" """
gatk --java-options "-Xmx${xmx_memory}G" -T HaplotypeCaller \ gatk --java-options "-Xmx${xmx_memory}G" -T HaplotypeCaller \
-nct ${task.cpus} \ -nct ${task.cpus} \
...@@ -34,7 +34,7 @@ process filter_snp { ...@@ -34,7 +34,7 @@ process filter_snp {
output: output:
tuple val(file_id), path("*_snp.vcf"), emit: vcf tuple val(file_id), path("*_snp.vcf"), emit: vcf
script: script:
xmx_memory = task.memory - ~/\s*GB/ xmx_memory = "${task.memory}" - ~/\s*GB/
""" """
gatk --java-options "-Xmx${xmx_memory}G" -T SelectVariants \ gatk --java-options "-Xmx${xmx_memory}G" -T SelectVariants \
-nct ${task.cpus} \ -nct ${task.cpus} \
...@@ -56,7 +56,7 @@ process filter_indels { ...@@ -56,7 +56,7 @@ process filter_indels {
output: output:
tuple val(file_id), path("*_indel.vcf"), emit: vcf tuple val(file_id), path("*_indel.vcf"), emit: vcf
script: script:
xmx_memory = task.memory - ~/\s*GB/ xmx_memory = "${task.memory}" - ~/\s*GB/
""" """
gatk --java-options "-Xmx${xmx_memory}G"-T SelectVariants \ gatk --java-options "-Xmx${xmx_memory}G"-T SelectVariants \
-nct ${task.cpus} \ -nct ${task.cpus} \
...@@ -80,7 +80,7 @@ process high_confidence_snp { ...@@ -80,7 +80,7 @@ process high_confidence_snp {
output: output:
tuple val(file_id), path("*_snp.vcf"), emit: vcf tuple val(file_id), path("*_snp.vcf"), emit: vcf
script: script:
xmx_memory = task.memory - ~/\s*GB/ xmx_memory = "${task.memory}" - ~/\s*GB/
""" """
gatk --java-options "-Xmx${xmx_memory}G"-T VariantFiltration \ gatk --java-options "-Xmx${xmx_memory}G"-T VariantFiltration \
-nct ${task.cpus} \ -nct ${task.cpus} \
...@@ -105,7 +105,7 @@ process high_confidence_indels { ...@@ -105,7 +105,7 @@ process high_confidence_indels {
output: output:
tuple val(file_id), path("*_indel.vcf"), emit: vcf tuple val(file_id), path("*_indel.vcf"), emit: vcf
script: script:
xmx_memory = task.memory - ~/\s*GB/ xmx_memory = "${task.memory}" - ~/\s*GB/
""" """
gatk --java-options "-Xmx${xmx_memory}G" -T VariantFiltration \ gatk --java-options "-Xmx${xmx_memory}G" -T VariantFiltration \
-nct ${task.cpus} \ -nct ${task.cpus} \
...@@ -128,7 +128,7 @@ process recalibrate_snp_table { ...@@ -128,7 +128,7 @@ process recalibrate_snp_table {
output: output:
tuple val(file_id), path("recal_data_table"), emit: recal_table tuple val(file_id), path("recal_data_table"), emit: recal_table
script: script:
xmx_memory = task.memory - ~/\s*GB/ xmx_memory = "${task.memory}" - ~/\s*GB/
""" """
gatk --java-options "-Xmx${xmx_memory}G" -T BaseRecalibrator \ gatk --java-options "-Xmx${xmx_memory}G" -T BaseRecalibrator \
-nct ${task.cpus} \ -nct ${task.cpus} \
...@@ -152,7 +152,7 @@ process recalibrate_snp { ...@@ -152,7 +152,7 @@ process recalibrate_snp {
output: output:
tuple val(file_id), path("*.bam"), emit: bam tuple val(file_id), path("*.bam"), emit: bam
script: script:
xmx_memory = task.memory - ~/\s*GB/ xmx_memory = "${task.memory}" - ~/\s*GB/
""" """
gatk --java-options "-Xmx${xmx_memory}G" -T PrintReads \ gatk --java-options "-Xmx${xmx_memory}G" -T PrintReads \
--use_jdk_deflater \ --use_jdk_deflater \
...@@ -176,7 +176,7 @@ process haplotype_caller { ...@@ -176,7 +176,7 @@ process haplotype_caller {
output: output:
tuple val(file_id), path("*.gvcf"), emit: gvcf tuple val(file_id), path("*.gvcf"), emit: gvcf
script: script:
xmx_memory = task.memory - ~/\s*GB/ xmx_memory = "${task.memory}" - ~/\s*GB/
""" """
gatk --java-options "-Xmx${xmx_memory}G" -T HaplotypeCaller \ gatk --java-options "-Xmx${xmx_memory}G" -T HaplotypeCaller \
-nct ${task.cpus} \ -nct ${task.cpus} \
...@@ -199,7 +199,7 @@ process gvcf_genotyping { ...@@ -199,7 +199,7 @@ process gvcf_genotyping {
output: output:
tuple val(file_id), path("*.vcf"), emit: vcf tuple val(file_id), path("*.vcf"), emit: vcf
script: script:
xmx_memory = task.memory - ~/\s*GB/ xmx_memory = "${task.memory}" - ~/\s*GB/
""" """
gatk --java-options "-Xmx${xmx_memory}G" -T GenotypeGVCFs \ gatk --java-options "-Xmx${xmx_memory}G" -T GenotypeGVCFs \
-nct ${task.cpus} \ -nct ${task.cpus} \
...@@ -220,7 +220,7 @@ process select_variants_snp { ...@@ -220,7 +220,7 @@ process select_variants_snp {
output: output:
tuple val(file_id), path("*_joint_snp.vcf"), emit: vcf tuple val(file_id), path("*_joint_snp.vcf"), emit: vcf
script: script:
xmx_memory = task.memory - ~/\s*GB/ xmx_memory = "${task.memory}" - ~/\s*GB/
""" """
gatk --java-options "-Xmx${xmx_memory}GG" -T SelectVariants \ gatk --java-options "-Xmx${xmx_memory}GG" -T SelectVariants \
-nct ${task.cpus} \ -nct ${task.cpus} \
...@@ -242,7 +242,7 @@ process select_variants_indels { ...@@ -242,7 +242,7 @@ process select_variants_indels {
output: output:
tuple val(file_id), path("*_joint_indel.vcf"), emit: vcf tuple val(file_id), path("*_joint_indel.vcf"), emit: vcf
script: script:
xmx_memory = task.memory - ~/\s*GB/ xmx_memory = "${task.memory}" - ~/\s*GB/
""" """
gatk --java-options "-Xmx${xmx_memory}G" -T SelectVariants \ gatk --java-options "-Xmx${xmx_memory}G" -T SelectVariants \
-nct ${task.cpus} \ -nct ${task.cpus} \
...@@ -265,7 +265,7 @@ process personalized_genome { ...@@ -265,7 +265,7 @@ process personalized_genome {
tuple val(file_id), path("*_genome.fasta"), emit: fasta tuple val(file_id), path("*_genome.fasta"), emit: fasta
script: script:
xmx_memory = task.memory - ~/\s*GB/ xmx_memory = "${task.memory}" - ~/\s*GB/
""" """
gatk --java-options "-Xmx${xmx_memory}G" -T FastaAlternateReferenceMaker\ gatk --java-options "-Xmx${xmx_memory}G" -T FastaAlternateReferenceMaker\
-R ${reference} \ -R ${reference} \
......
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