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Fix annotsv #37

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Merged
nourmahfel merged 2 commits into from
Mar 24, 2026
Merged

Fix annotsv #37

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d186aca
Fix annotsv
nourmahfel Mar 24, 2026
51fd454
Fix annotsv
nourmahfel Mar 24, 2026
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14 changes: 7 additions & 7 deletions conf/base.config
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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 }
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46 changes: 26 additions & 20 deletions conf/modules.config
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Expand Up @@ -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 = [
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