diff --git a/README.md b/README.md index 9f81360..ef731d6 100644 --- a/README.md +++ b/README.md @@ -80,6 +80,7 @@ Optional input: * --snpeff_organism: the SnpEff organism name (eg: hg19, hg38, GRCh37.75, GRCh38.99) * --snpeff_datadir: the SnpEff data folder where the reference genomes were previously downloaded. Required if --snpeff_organism is provided * --snpeff_args: additional SnpEff arguments + * --snpeff_memory: for some samples SnpEff may require to use more memory (default: 3g) * --mapping_quality: VAFator minimum mapping quality (default: 0) * --base_call_quality: VAFator minimum base call quality (default: 0) diff --git a/modules/05_variant_annotation.nf b/modules/05_variant_annotation.nf index a520b2d..b469ae1 100644 --- a/modules/05_variant_annotation.nf +++ b/modules/05_variant_annotation.nf @@ -1,3 +1,4 @@ +params.snpeff_memory = "3g" params.memory = "3g" params.cpus = 1 params.output = "." @@ -8,8 +9,9 @@ params.snpeff_args = "" process VARIANT_ANNOTATION_SNPEFF { cpus params.cpus - memory params.memory + memory params.snpeff_memory publishDir "${params.output}/${name}", mode: "copy" + tag "${name}" conda (params.enable_conda ? "bioconda::snpeff=5.0" : null) @@ -22,7 +24,9 @@ process VARIANT_ANNOTATION_SNPEFF { script: datadir_arg = params.snpeff_datadir ? "-dataDir ${params.snpeff_datadir}" : "" """ - snpEff eff ${datadir_arg} ${params.snpeff_args} -nodownload ${params.snpeff_organism} ${vcf} > ${name}.annotated.vcf + snpEff -Xmx${params.snpeff_memory} eff \ + ${datadir_arg} ${params.snpeff_args} \ + -nodownload ${params.snpeff_organism} ${vcf} > ${name}.annotated.vcf """ } @@ -30,6 +34,7 @@ process VARIANT_ANNOTATION_BCFTOOLS { cpus params.cpus memory params.memory publishDir "${params.output}/${name}", mode: "copy" + tag "${name}" conda (params.enable_conda ? "conda-forge::libgcc-ng=10.3.0 conda-forge::gsl=2.7 bioconda::bcftools=1.15.1" : null) diff --git a/nextflow.config b/nextflow.config index dfe94f5..57fddf6 100644 --- a/nextflow.config +++ b/nextflow.config @@ -27,7 +27,7 @@ env { // Capture exit codes from upstream processes when piping process.shell = ['/bin/bash', '-euo', 'pipefail'] -VERSION = '2.4.0' +VERSION = '2.4.1' manifest { name = 'TRON-Bioinformatics/tronflow-vcf-postprocessing' @@ -84,6 +84,7 @@ Optional input: * --snpeff_organism: the SnpEff organism name (eg: hg19, hg38, GRCh37.75, GRCh38.99) * --snpeff_datadir: the SnpEff data folder where the reference genomes were previously downloaded. Required if --snpeff_organism is provided * --snpeff_args: additional SnpEff arguments + * --snpeff_memory: for some samples SnpEff may require to use more memory (default: 3g) * --mapping_quality: VAFator minimum mapping quality (default: 0) * --base_call_quality: VAFator minimum base call quality (default: 0)