diff --git a/src/nf_modules/gatk4/main.nf b/src/nf_modules/gatk4/main.nf index 4e77d5cad074261b0b4245d0f1071638a7d44563..0a468ca576f2a7e5231fb0b1484f29a183c4081e 100644 --- a/src/nf_modules/gatk4/main.nf +++ b/src/nf_modules/gatk4/main.nf @@ -13,7 +13,7 @@ process variant_calling { tuple val(file_id), path("*.vcf"), emit: vcf script: - xmx_memory = task.memory - ~/\s*GB/ + xmx_memory = "${task.memory}" - ~/\s*GB/ """ gatk --java-options "-Xmx${xmx_memory}G" -T HaplotypeCaller \ -nct ${task.cpus} \ @@ -34,7 +34,7 @@ process filter_snp { output: tuple val(file_id), path("*_snp.vcf"), emit: vcf script: - xmx_memory = task.memory - ~/\s*GB/ + xmx_memory = "${task.memory}" - ~/\s*GB/ """ gatk --java-options "-Xmx${xmx_memory}G" -T SelectVariants \ -nct ${task.cpus} \ @@ -56,7 +56,7 @@ process filter_indels { output: tuple val(file_id), path("*_indel.vcf"), emit: vcf script: - xmx_memory = task.memory - ~/\s*GB/ + xmx_memory = "${task.memory}" - ~/\s*GB/ """ gatk --java-options "-Xmx${xmx_memory}G"-T SelectVariants \ -nct ${task.cpus} \ @@ -80,7 +80,7 @@ process high_confidence_snp { output: tuple val(file_id), path("*_snp.vcf"), emit: vcf script: - xmx_memory = task.memory - ~/\s*GB/ + xmx_memory = "${task.memory}" - ~/\s*GB/ """ gatk --java-options "-Xmx${xmx_memory}G"-T VariantFiltration \ -nct ${task.cpus} \ @@ -105,7 +105,7 @@ process high_confidence_indels { output: tuple val(file_id), path("*_indel.vcf"), emit: vcf script: - xmx_memory = task.memory - ~/\s*GB/ + xmx_memory = "${task.memory}" - ~/\s*GB/ """ gatk --java-options "-Xmx${xmx_memory}G" -T VariantFiltration \ -nct ${task.cpus} \ @@ -128,7 +128,7 @@ process recalibrate_snp_table { output: tuple val(file_id), path("recal_data_table"), emit: recal_table script: - xmx_memory = task.memory - ~/\s*GB/ + xmx_memory = "${task.memory}" - ~/\s*GB/ """ gatk --java-options "-Xmx${xmx_memory}G" -T BaseRecalibrator \ -nct ${task.cpus} \ @@ -152,7 +152,7 @@ process recalibrate_snp { output: tuple val(file_id), path("*.bam"), emit: bam script: - xmx_memory = task.memory - ~/\s*GB/ + xmx_memory = "${task.memory}" - ~/\s*GB/ """ gatk --java-options "-Xmx${xmx_memory}G" -T PrintReads \ --use_jdk_deflater \ @@ -176,7 +176,7 @@ process haplotype_caller { output: tuple val(file_id), path("*.gvcf"), emit: gvcf script: - xmx_memory = task.memory - ~/\s*GB/ + xmx_memory = "${task.memory}" - ~/\s*GB/ """ gatk --java-options "-Xmx${xmx_memory}G" -T HaplotypeCaller \ -nct ${task.cpus} \ @@ -199,7 +199,7 @@ process gvcf_genotyping { output: tuple val(file_id), path("*.vcf"), emit: vcf script: - xmx_memory = task.memory - ~/\s*GB/ + xmx_memory = "${task.memory}" - ~/\s*GB/ """ gatk --java-options "-Xmx${xmx_memory}G" -T GenotypeGVCFs \ -nct ${task.cpus} \ @@ -220,7 +220,7 @@ process select_variants_snp { output: tuple val(file_id), path("*_joint_snp.vcf"), emit: vcf script: - xmx_memory = task.memory - ~/\s*GB/ + xmx_memory = "${task.memory}" - ~/\s*GB/ """ gatk --java-options "-Xmx${xmx_memory}GG" -T SelectVariants \ -nct ${task.cpus} \ @@ -242,7 +242,7 @@ process select_variants_indels { output: tuple val(file_id), path("*_joint_indel.vcf"), emit: vcf script: - xmx_memory = task.memory - ~/\s*GB/ + xmx_memory = "${task.memory}" - ~/\s*GB/ """ gatk --java-options "-Xmx${xmx_memory}G" -T SelectVariants \ -nct ${task.cpus} \ @@ -265,7 +265,7 @@ process personalized_genome { tuple val(file_id), path("*_genome.fasta"), emit: fasta script: - xmx_memory = task.memory - ~/\s*GB/ + xmx_memory = "${task.memory}" - ~/\s*GB/ """ gatk --java-options "-Xmx${xmx_memory}G" -T FastaAlternateReferenceMaker\ -R ${reference} \