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nf-configs
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kevbrick-patch-1
pierrespc 3 years ago
parent 136fd44e0c
commit e5d4a357c5
6 changed files with 111 additions and 121 deletions
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2
conf/maestro.config
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@ -1,6 +1,6 @@
params {
config_profile_description = 'Institut Pasteur Maestro cluster profile'
config_profile_url = 'https://confluence.pasteur.fr/spaces/viewspace.action?key=FAQA'
config_profile_url = 'https://research.pasteur.fr/en/equipment/maestro-compute-cluster/'
config_profile_contact = 'Pierre Luisi (@pierrespc)'
}

107
conf/pipeline/eager/maestro.config
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/*
* -------------------------------------------------
* Nextflow config file for running nf-core eager on whole genome data or mitogenomes
* -------------------------------------------------
* nextflow run nf-core/eager -profile maestro,<qos>,maestro,<genome> (where <qos> is long or normal and <genome> is nuclear or mitocondrial)
*/
params {
config_profile_name = 'nf-core/eager nuclear/mitocondrial - human profiles'
config_profile_description = "Simple profiles for human nuclear or mito genomes"
email = 'pluisi@pasteur.fr'
}
profiles {
nuclear {
process {
errorStrategy = 'retry'
maxRetries = 2
withName:'makeBWAIndex'{
cpus = { check_max( 8 * task.attempt, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { check_max( 12.h * task.attempt, 'time' ) }
}
withName:'adapter_removal'{
cpus = { check_max( 8 * task.attempt, 'cpus' ) }
memory = { check_max( 16.GB * task.attempt, 'memory' ) }
time = { check_max( 12.h * task.attempt, 'time' ) }
}
withName:'bwa'{
cpus = { check_max( 30 * task.attempt, 'cpus' ) }
memory = { check_max( 40.GB * task.attempt, 'memory' ) }
time = 24.h
}
withName:'markduplicates'{
errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' }
cpus = { check_max( 8 * task.attempt, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { check_max( 6.h * task.attempt, 'time' ) }
}
withName:'damageprofiler'{
cpus = 1
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { check_max( 6.h * task.attempt, 'time' ) }
}
withName:'fastp'{
cpus = 8
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { check_max( 6.h * task.attempt, 'time' ) }
}
withName:'fastqc'{
cpus = 2
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { check_max( 6.h * task.attempt, 'time' ) }
}
}
}
mitocondrial {
process {
errorStrategy = 'retry'
maxRetries = 2
withName:'makeBWAIndex'{
cpus = { check_max( 8 * task.attempt, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { check_max( 12.h * task.attempt, 'time' ) }
}
withName:'adapter_removal'{
cpus = { check_max( 8 * task.attempt, 'cpus' ) }
memory = { check_max( 16.GB * task.attempt, 'memory' ) }
time = { check_max( 12.h * task.attempt, 'time' ) }
}
withName:'bwa'{
cpus = { check_max( 5 * task.attempt, 'cpus' ) }
memory = { check_max( 5.GB * task.attempt, 'memory' ) }
time = 24.h
}
withName:'markduplicates'{
errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' }
cpus = { check_max( 5 * task.attempt, 'cpus' ) }
memory = { check_max( 5.GB * task.attempt, 'memory' ) }
time = { check_max( 6.h * task.attempt, 'time' ) }
}
withName:'damageprofiler'{
cpus = 1
memory = { check_max( 5.GB * task.attempt, 'memory' ) }
time = { check_max( 3.h * task.attempt, 'time' ) }
}
withName:'fastp'{
cpus = 8
memory = { check_max( 5.GB * task.attempt, 'memory' ) }
time = { check_max( 3.h * task.attempt, 'time' ) }
}
withName:'fastqc'{
cpus = 2
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { check_max( 6.h * task.attempt, 'time' ) }
}
}
}
}

58
conf/pipeline/eager/maestromitocondrial.config
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@ -1,58 +0,0 @@
/*
* -------------------------------------------------
* Nextflow config file for running nf-core eager on mitocondrial data (providing reference genome only the reference genome for mitogenomes)_
* -------------------------------------------------
* nextflow run nf-core/eager -profile maestro,<qos>,maestromitocondrial (where <qos> is long or normal)
*/
params {
config_profile_name = 'nf-core/eager mitrocondrial - human profile'
config_profile_description = "A simple profile for human mitogenomes"
email = 'pluisi@pasteur.fr'
}
process {
errorStrategy = 'retry'
maxRetries = 2
withName:'makeBWAIndex'{
cpus = { check_max( 8 * task.attempt, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { check_max( 12.h * task.attempt, 'time' ) }
}
withName:'adapter_removal'{
cpus = { check_max( 8 * task.attempt, 'cpus' ) }
memory = { check_max( 16.GB * task.attempt, 'memory' ) }
time = { check_max( 12.h * task.attempt, 'time' ) }
}
withName:'bwa'{
cpus = { check_max( 5 * task.attempt, 'cpus' ) }
memory = { check_max( 5.GB * task.attempt, 'memory' ) }
time = 24.h
}
withName:'markduplicates'{
errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' }
cpus = { check_max( 5 * task.attempt, 'cpus' ) }
memory = { check_max( 5.GB * task.attempt, 'memory' ) }
time = { check_max( 6.h * task.attempt, 'time' ) }
}
withName:'damageprofiler'{
cpus = 1
memory = { check_max( 5.GB * task.attempt, 'memory' ) }
time = { check_max( 3.h * task.attempt, 'time' ) }
}
withName:'fastp'{
cpus = 8
memory = { check_max( 5.GB * task.attempt, 'memory' ) }
time = { check_max( 3.h * task.attempt, 'time' ) }
}
withName:'fastqc'{
cpus = 2
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { check_max( 6.h * task.attempt, 'time' ) }
}
}

58
conf/pipeline/eager/maestronuclear.config
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/*
* -------------------------------------------------
* Nextflow config file for running nf-core eager on whole genome data
* -------------------------------------------------
* nextflow run nf-core/eager -profile maestro,<qos>,maestronuclear (where <qos> is long or normal)
*/
params {
config_profile_name = 'nf-core/eager nucleaer - human profile'
config_profile_description = "A simple profile for human nuclear genomes"
email = 'pluisi@pasteur.fr'
}
process {
errorStrategy = 'retry'
maxRetries = 2
withName:'makeBWAIndex'{
cpus = { check_max( 8 * task.attempt, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { check_max( 12.h * task.attempt, 'time' ) }
}
withName:'adapter_removal'{
cpus = { check_max( 8 * task.attempt, 'cpus' ) }
memory = { check_max( 16.GB * task.attempt, 'memory' ) }
time = { check_max( 12.h * task.attempt, 'time' ) }
}
withName:'bwa'{
cpus = { check_max( 15 * task.attempt, 'cpus' ) }
memory = { check_max( 16.GB * task.attempt, 'memory' ) }
time = 24.h
}
withName:'markduplicates'{
errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' }
cpus = { check_max( 8 * task.attempt, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { check_max( 6.h * task.attempt, 'time' ) }
}
withName:'damageprofiler'{
cpus = 1
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { check_max( 6.h * task.attempt, 'time' ) }
}
withName:'fastp'{
cpus = 8
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { check_max( 6.h * task.attempt, 'time' ) }
}
withName:'fastqc'{
cpus = 2
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { check_max( 6.h * task.attempt, 'time' ) }
}
}

4
docs/maestro.md
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@ -4,7 +4,7 @@ If you are using TARS cluster, please refer to pasteur profile.
This is an intent for configuration of nf-core in Maestro cluster on the normal or long qos depending on the ressources required
I am not expert of nf-core so pelase refer to docs/pasteur.md for installing and running nf-core
Please refer to docs/pasteur.md for installing and running nf-core instructions.
Run the pipeline with `-profile maestro,<qos>` where qos is long or normal
Run the pipeline with -profile maestro,<qos> where qos is long or normal.

3
pipeline/eager.config
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profiles {
mpcdf { includeConfig "${params.custom_config_base}/conf/pipeline/eager/mpcdf.config" }
eva { includeConfig "${params.custom_config_base}/conf/pipeline/eager/eva.config" }
maestronuclear { includeConfig "${params.custom_config_base}/conf/pipeline/eager/maestronuclear.config" }
maestromitocondrial { includeConfig "${params.custom_config_base}/conf/pipeline/eager/maestromitocondrial.config" }
maestro { includeConfig "${params.custom_config_base}/conf/pipeline/eager/maestro.config" }
}

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