diff --git a/conf/base.config b/conf/base.config index 6b4280b..9357bb6 100644 --- a/conf/base.config +++ b/conf/base.config @@ -8,6 +8,13 @@ ---------------------------------------------------------------------------------------- */ + +executor { + cpus = 36 // Total CPUs available on your system + memory = '216.GB' // Total memory available on your system + queueSize = 10 // Max number of tasks that can be queued/running +} + process { // TODO nf-core: Check the defaults for all processes @@ -19,13 +26,6 @@ process { maxRetries = 1 maxErrors = '-1' - // Process-specific resource requirements - // NOTE - Please try and reuse the labels below as much as possible. - // These labels are used and recognised by default in DSL2 files hosted on nf-core/modules. - // If possible, it would be nice to keep the same label naming convention when - // adding in your local modules too. - // TODO nf-core: Customise requirements for specific processes. - // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors withLabel:process_single { cpus = { 1 } memory = { 6.GB * task.attempt } diff --git a/conf/modules.config b/conf/modules.config index cd898a5..450c4f4 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -666,29 +666,35 @@ process { } - withName: 'ANNOTSV_SNIFFLES' { - containerOptions = { - workflow.containerEngine == 'docker' ? '--user root' : '' + withName: 'ANNOTSV_SNIFFLES' { + label = 'process_high' + containerOptions = { + workflow.containerEngine == 'singularity' ? + '--writable-tmpfs --bind $PWD --env HOME=$PWD --env TMPDIR=$PWD --env TMP=$PWD' : + '--user root' } - ext.args = { meta.hpo_terms ? "-vcf 1 -genomeBuild GRCh38 -rankFiltering ${params.rankfiltering} -hpo '${meta.hpo_terms}'" : "-vcf 1 -genomeBuild GRCh38" } - ext.prefix = { "${meta.id}_annotsv" } - publishDir = [ - path: { "${params.outdir}/${meta.id}/annotsv_sniffles" }, - mode: 'copy' - ] - } + ext.args = { meta.hpo_terms ? "-vcf 1 -genomeBuild GRCh38 -rankFiltering ${params.rankfiltering} -hpo '${meta.hpo_terms}'" : "-vcf 1 -genomeBuild GRCh38" } + ext.prefix = { "${meta.id}_annotsv" } + publishDir = [ + path: { "${params.outdir}/${meta.id}/annotsv_sniffles" }, + mode: 'copy' + ] + } - withName: 'ANNOTSV_SVIM' { - containerOptions = { - workflow.containerEngine == 'docker' ? '--user root' : '' +withName: 'ANNOTSV_SVIM' { + label = 'process_high' + containerOptions = { + workflow.containerEngine == 'singularity' ? + '--writable-tmpfs --bind $PWD --env HOME=$PWD --env TMPDIR=$PWD --env TMP=$PWD' : + '--user root' } - ext.args = { meta.hpo_terms ? "-vcf 1 -genomeBuild GRCh38 -rankFiltering ${params.rankfiltering} -hpo '${meta.hpo_terms}'" : "-vcf 1 -genomeBuild GRCh38" } - ext.prefix = { "${meta.id}_annotsv" } - publishDir = [ - path: { "${params.outdir}/${meta.id}/annotsv_svim" }, - mode: 'copy' - ] - } + ext.args = { meta.hpo_terms ? "-vcf 1 -genomeBuild GRCh38 -rankFiltering ${params.rankfiltering} -hpo '${meta.hpo_terms}'" : "-vcf 1 -genomeBuild GRCh38" } + ext.prefix = { "${meta.id}_annotsv" } + publishDir = [ + path: { "${params.outdir}/${meta.id}/annotsv_svim" }, + mode: 'copy' + ] + } withName: 'UNTAR_ANNOTSV' { publishDir = [