millironx/nf-configs
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long and normal qos profiles defined now in an unique maestro config file. maestro.config also defined in pipeline/eager for ressources assignation to specific processes

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pierrespc 2021-09-29 13:11:14 +02:00
parent 3e22b85b02
commit 9ea3e2096a
3 changed files with 96 additions and 12 deletions
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23
conf/maestro.config
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@ -10,6 +10,9 @@ singularity {
runOptions = '--home $HOME:/home/$USER --bind /pasteur'
}
profiles {
normal {
process {
executor = 'slurm'
scratch = false
@ -24,3 +27,23 @@ params {
max_cpus = 96
max_time = 24.h
}
}
long {
process {
executor = 'slurm'
scratch = false
queue = 'common'
clusterOptions = '--qos=long'
}
params {
igenomes_ignore = true
igenomesIgnore = true
max_memory = 400.GB
max_cpus = 5
max_time = 8760.h
}
}
}

60
conf/pipeline/eager/maestro.config Normal file
View file

@ -0,0 +1,60 @@
/*
* -------------------------------------------------
* Nextflow config file for running tests
* -------------------------------------------------
* Defines bundled input files and everything required
* to run a fast and simple test. Use as follows:
* nextflow run nf-core/eager -profile test, docker (or singularity, or conda)
*/
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' ) }
}
}

1
pipeline/eager.config
View file

@ -11,4 +11,5 @@
profiles {
mpcdf { includeConfig "${params.custom_config_base}/conf/pipeline/eager/mpcdf.config" }
eva { includeConfig "${params.custom_config_base}/conf/pipeline/eager/eva.config" }
maestro { includeConfig "${params.custom_config_base}/conf/maestro.config" }
}