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clean doc
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pierrespc
parent
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commit
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6 changed files with 111 additions and 121 deletions
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@ -1,6 +1,6 @@
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params {
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params {
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config_profile_description = 'Institut Pasteur Maestro cluster profile'
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config_profile_description = 'Institut Pasteur Maestro cluster profile'
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config_profile_url = 'https://confluence.pasteur.fr/spaces/viewspace.action?key=FAQA'
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config_profile_url = 'https://research.pasteur.fr/en/equipment/maestro-compute-cluster/'
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config_profile_contact = 'Pierre Luisi (@pierrespc)'
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config_profile_contact = 'Pierre Luisi (@pierrespc)'
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}
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}
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107
conf/pipeline/eager/maestro.config
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107
conf/pipeline/eager/maestro.config
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/*
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* -------------------------------------------------
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* Nextflow config file for running nf-core eager on whole genome data or mitogenomes
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* -------------------------------------------------
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* nextflow run nf-core/eager -profile maestro,<qos>,maestro,<genome> (where <qos> is long or normal and <genome> is nuclear or mitocondrial)
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*/
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params {
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config_profile_name = 'nf-core/eager nuclear/mitocondrial - human profiles'
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config_profile_description = "Simple profiles for human nuclear or mito genomes"
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email = 'pluisi@pasteur.fr'
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}
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profiles {
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nuclear {
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process {
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errorStrategy = 'retry'
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maxRetries = 2
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withName:'makeBWAIndex'{
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cpus = { check_max( 8 * task.attempt, 'cpus' ) }
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memory = { check_max( 8.GB * task.attempt, 'memory' ) }
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time = { check_max( 12.h * task.attempt, 'time' ) }
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}
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withName:'adapter_removal'{
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cpus = { check_max( 8 * task.attempt, 'cpus' ) }
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memory = { check_max( 16.GB * task.attempt, 'memory' ) }
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time = { check_max( 12.h * task.attempt, 'time' ) }
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}
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withName:'bwa'{
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cpus = { check_max( 30 * task.attempt, 'cpus' ) }
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memory = { check_max( 40.GB * task.attempt, 'memory' ) }
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time = 24.h
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}
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withName:'markduplicates'{
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errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' }
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cpus = { check_max( 8 * task.attempt, 'cpus' ) }
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memory = { check_max( 8.GB * task.attempt, 'memory' ) }
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time = { check_max( 6.h * task.attempt, 'time' ) }
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}
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withName:'damageprofiler'{
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cpus = 1
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memory = { check_max( 8.GB * task.attempt, 'memory' ) }
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time = { check_max( 6.h * task.attempt, 'time' ) }
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}
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withName:'fastp'{
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cpus = 8
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memory = { check_max( 8.GB * task.attempt, 'memory' ) }
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time = { check_max( 6.h * task.attempt, 'time' ) }
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}
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withName:'fastqc'{
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cpus = 2
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memory = { check_max( 8.GB * task.attempt, 'memory' ) }
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time = { check_max( 6.h * task.attempt, 'time' ) }
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}
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}
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}
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mitocondrial {
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process {
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errorStrategy = 'retry'
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maxRetries = 2
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withName:'makeBWAIndex'{
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cpus = { check_max( 8 * task.attempt, 'cpus' ) }
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memory = { check_max( 8.GB * task.attempt, 'memory' ) }
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time = { check_max( 12.h * task.attempt, 'time' ) }
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}
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withName:'adapter_removal'{
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cpus = { check_max( 8 * task.attempt, 'cpus' ) }
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memory = { check_max( 16.GB * task.attempt, 'memory' ) }
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time = { check_max( 12.h * task.attempt, 'time' ) }
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}
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withName:'bwa'{
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cpus = { check_max( 5 * task.attempt, 'cpus' ) }
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memory = { check_max( 5.GB * task.attempt, 'memory' ) }
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time = 24.h
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}
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withName:'markduplicates'{
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errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' }
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cpus = { check_max( 5 * task.attempt, 'cpus' ) }
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memory = { check_max( 5.GB * task.attempt, 'memory' ) }
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time = { check_max( 6.h * task.attempt, 'time' ) }
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}
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withName:'damageprofiler'{
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cpus = 1
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memory = { check_max( 5.GB * task.attempt, 'memory' ) }
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time = { check_max( 3.h * task.attempt, 'time' ) }
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}
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withName:'fastp'{
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cpus = 8
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memory = { check_max( 5.GB * task.attempt, 'memory' ) }
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time = { check_max( 3.h * task.attempt, 'time' ) }
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}
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withName:'fastqc'{
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cpus = 2
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memory = { check_max( 8.GB * task.attempt, 'memory' ) }
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time = { check_max( 6.h * task.attempt, 'time' ) }
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}
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}
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}
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}
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@ -1,58 +0,0 @@
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/*
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* -------------------------------------------------
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* Nextflow config file for running nf-core eager on mitocondrial data (providing reference genome only the reference genome for mitogenomes)_
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* -------------------------------------------------
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* nextflow run nf-core/eager -profile maestro,<qos>,maestromitocondrial (where <qos> is long or normal)
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*/
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params {
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config_profile_name = 'nf-core/eager mitrocondrial - human profile'
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config_profile_description = "A simple profile for human mitogenomes"
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email = 'pluisi@pasteur.fr'
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}
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process {
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errorStrategy = 'retry'
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maxRetries = 2
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withName:'makeBWAIndex'{
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cpus = { check_max( 8 * task.attempt, 'cpus' ) }
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memory = { check_max( 8.GB * task.attempt, 'memory' ) }
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time = { check_max( 12.h * task.attempt, 'time' ) }
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}
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withName:'adapter_removal'{
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cpus = { check_max( 8 * task.attempt, 'cpus' ) }
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memory = { check_max( 16.GB * task.attempt, 'memory' ) }
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time = { check_max( 12.h * task.attempt, 'time' ) }
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}
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withName:'bwa'{
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cpus = { check_max( 5 * task.attempt, 'cpus' ) }
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memory = { check_max( 5.GB * task.attempt, 'memory' ) }
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time = 24.h
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}
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withName:'markduplicates'{
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errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' }
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cpus = { check_max( 5 * task.attempt, 'cpus' ) }
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memory = { check_max( 5.GB * task.attempt, 'memory' ) }
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time = { check_max( 6.h * task.attempt, 'time' ) }
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}
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withName:'damageprofiler'{
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cpus = 1
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memory = { check_max( 5.GB * task.attempt, 'memory' ) }
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time = { check_max( 3.h * task.attempt, 'time' ) }
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}
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withName:'fastp'{
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cpus = 8
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memory = { check_max( 5.GB * task.attempt, 'memory' ) }
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time = { check_max( 3.h * task.attempt, 'time' ) }
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}
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withName:'fastqc'{
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cpus = 2
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memory = { check_max( 8.GB * task.attempt, 'memory' ) }
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time = { check_max( 6.h * task.attempt, 'time' ) }
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}
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}
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@ -1,58 +0,0 @@
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/*
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* -------------------------------------------------
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* Nextflow config file for running nf-core eager on whole genome data
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* -------------------------------------------------
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* nextflow run nf-core/eager -profile maestro,<qos>,maestronuclear (where <qos> is long or normal)
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*/
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params {
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config_profile_name = 'nf-core/eager nucleaer - human profile'
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config_profile_description = "A simple profile for human nuclear genomes"
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email = 'pluisi@pasteur.fr'
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}
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process {
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errorStrategy = 'retry'
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maxRetries = 2
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withName:'makeBWAIndex'{
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cpus = { check_max( 8 * task.attempt, 'cpus' ) }
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memory = { check_max( 8.GB * task.attempt, 'memory' ) }
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time = { check_max( 12.h * task.attempt, 'time' ) }
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}
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withName:'adapter_removal'{
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cpus = { check_max( 8 * task.attempt, 'cpus' ) }
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memory = { check_max( 16.GB * task.attempt, 'memory' ) }
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time = { check_max( 12.h * task.attempt, 'time' ) }
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}
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withName:'bwa'{
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cpus = { check_max( 15 * task.attempt, 'cpus' ) }
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memory = { check_max( 16.GB * task.attempt, 'memory' ) }
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time = 24.h
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}
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withName:'markduplicates'{
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errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' }
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cpus = { check_max( 8 * task.attempt, 'cpus' ) }
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memory = { check_max( 8.GB * task.attempt, 'memory' ) }
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time = { check_max( 6.h * task.attempt, 'time' ) }
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}
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withName:'damageprofiler'{
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cpus = 1
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memory = { check_max( 8.GB * task.attempt, 'memory' ) }
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time = { check_max( 6.h * task.attempt, 'time' ) }
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}
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withName:'fastp'{
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cpus = 8
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memory = { check_max( 8.GB * task.attempt, 'memory' ) }
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time = { check_max( 6.h * task.attempt, 'time' ) }
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}
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withName:'fastqc'{
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cpus = 2
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memory = { check_max( 8.GB * task.attempt, 'memory' ) }
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time = { check_max( 6.h * task.attempt, 'time' ) }
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}
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}
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@ -4,7 +4,7 @@ If you are using TARS cluster, please refer to pasteur profile.
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This is an intent for configuration of nf-core in Maestro cluster on the normal or long qos depending on the ressources required
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This is an intent for configuration of nf-core in Maestro cluster on the normal or long qos depending on the ressources required
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I am not expert of nf-core so pelase refer to docs/pasteur.md for installing and running nf-core
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Please refer to docs/pasteur.md for installing and running nf-core instructions.
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Run the pipeline with `-profile maestro,<qos>` where qos is long or normal
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Run the pipeline with -profile maestro,<qos> where qos is long or normal.
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@ -11,6 +11,5 @@
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profiles {
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profiles {
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mpcdf { includeConfig "${params.custom_config_base}/conf/pipeline/eager/mpcdf.config" }
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mpcdf { includeConfig "${params.custom_config_base}/conf/pipeline/eager/mpcdf.config" }
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eva { includeConfig "${params.custom_config_base}/conf/pipeline/eager/eva.config" }
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eva { includeConfig "${params.custom_config_base}/conf/pipeline/eager/eva.config" }
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maestronuclear { includeConfig "${params.custom_config_base}/conf/pipeline/eager/maestronuclear.config" }
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maestro { includeConfig "${params.custom_config_base}/conf/pipeline/eager/maestro.config" }
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maestromitocondrial { includeConfig "${params.custom_config_base}/conf/pipeline/eager/maestromitocondrial.config" }
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}
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}
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