mirror of
https://github.com/MillironX/nf-configs.git
synced 2024-11-24 17:19:54 +00:00
clean doc
This commit is contained in:
pierrespc
parent
136fd44e0c
commit
e5d4a357c5
6 changed files with 111 additions and 121 deletions
|
|
@ -1,6 +1,6 @@
|
||||||
params {
|
params {
|
||||||
config_profile_description = 'Institut Pasteur Maestro cluster profile'
|
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)'
|
config_profile_contact = 'Pierre Luisi (@pierrespc)'
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
|
||||||
107
conf/pipeline/eager/maestro.config
Normal file
107
conf/pipeline/eager/maestro.config
Normal file
|
|
@ -0,0 +1,107 @@
|
||||||
|
/*
|
||||||
|
* -------------------------------------------------
|
||||||
|
* 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' ) }
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
@ -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' ) }
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
@ -1,58 +0,0 @@
|
||||||
/*
|
|
||||||
* -------------------------------------------------
|
|
||||||
* 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' ) }
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
@ -4,7 +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
|
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.
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -11,6 +11,5 @@
|
||||||
profiles {
|
profiles {
|
||||||
mpcdf { includeConfig "${params.custom_config_base}/conf/pipeline/eager/mpcdf.config" }
|
mpcdf { includeConfig "${params.custom_config_base}/conf/pipeline/eager/mpcdf.config" }
|
||||||
eva { includeConfig "${params.custom_config_base}/conf/pipeline/eager/eva.config" }
|
eva { includeConfig "${params.custom_config_base}/conf/pipeline/eager/eva.config" }
|
||||||
maestronuclear { includeConfig "${params.custom_config_base}/conf/pipeline/eager/maestronuclear.config" }
|
maestro { includeConfig "${params.custom_config_base}/conf/pipeline/eager/maestro.config" }
|
||||||
maestromitocondrial { includeConfig "${params.custom_config_base}/conf/pipeline/eager/maestromitocondrial.config" }
|
|
||||||
}
|
}
|
||||||
|
|
|
||||||
Loading…
Reference in a new issue