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base.config
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base.config
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/* -------------------------------------------------
* Base Nextflow config file
* -------------------------------------------------
* This file contains basic process requirement setup. It DOES NOT
* contain any config for cluster, so will run in default mode by
* itself. It should be used with the max_memory, max_cpus and
* max_time params for customising hardware limits
*/
process {
cpus = 1
memory = { check_max( 10.GB * task.attempt, 'memory' ) }
time = { check_max( 2.h * task.attempt, 'time' ) }
errorStrategy = { task.exitStatus in [140,143,137,104,134,139] ? 'retry' : 'finish' }
maxRetries = 3
maxErrors = '-1'
// Process-specific resource requirements
withName:"DECONT" {
container = 'lichenhao/shotgunmetagenomics-decont:v0.0.1'
time = { check_max( 6.h * task.attempt, 'time') }
cpus = { check_max(12, 'cpus') }
memory = { check_max( 16.GB * task.attempt, 'memory') }
}
withName:"KRAKEN2" {
container = 'lichenhao/shotgunmetagenomics-kraken2:v2.0.8'
time = { check_max( 4.h * task.attempt, 'time') }
cpus = { check_max(4, 'cpus') }
}
withName:"BRACKEN" {
container = 'lichenhao/shotgunmetagenomics-kraken2:v2.0.8'
time = { check_max( 4.h * task.attempt, 'time') }
cpus = 1
memory = { check_max( 4.GB * task.attempt, 'memory') }
}
withName:"METAPHLAN2" {
container = 'lichenhao/shotgunmetagenomics-metaphlan2:2.7.7'
time = { check_max( 4.h * task.attempt, 'time') }
cpus = { check_max(8, 'cpus') }
memory = { check_max( 14.GB * task.attempt, 'memory') }
}
withName:"SAMPLE2MARKER" {
container = 'lichenhao/shotgunmetagenomics-metaphlan2:2.7.7'
time = { check_max( 4.h * task.attempt, 'time') }
memory = { check_max( 10.GB * task.attempt, 'memory') }
}
withName:"STRAINPHLAN" {
container = 'lichenhao/shotgunmetagenomics-metaphlan2:2.7.7'
time = { check_max( 24.h * task.attempt, 'time') }
cpus = { check_max(8, 'cpus') }
memory = { check_max( 10.GB * task.attempt, 'memory') }
}
withName:"HUMANN2_INDEX" {
container = 'lichenhao/shotgunmetagenomics-humann2_mini:v2.8.1'
time = { check_max( 4.h * task.attempt, 'time') }
cpus = 1
memory = { check_max( 7.GB * task.attempt, 'memory') }
}
withName:"HUMANN2" {
container = 'lichenhao/shotgunmetagenomics-humann2_mini:v2.8.1'
time = { check_max( 4.h * task.attempt, 'time') }
cpus = { check_max(8, 'cpus') }
memory = { check_max( 15.GB * task.attempt, 'memory') }
maxForks = 20 // HUMAnN2 still produces a large intermediate file, limit the number of processes running in parallel
}
withName:"SPLIT_.*" {
//container = 'ubuntu' // uncomment this line and comment next line if you want to execute this step on cloud
executor = 'local'
time = { check_max( 1.h * task.attempt, 'time') }
cpus = 1
memory = { check_max( 2.GB * task.attempt, 'memory') }
}
withName:"SRST2" {
container = 'quay.io/biocontainers/srst2:0.2.0--py27_2'
time = { check_max( 4.h * task.attempt, 'time') }
cpus = { check_max(8, 'cpus') }
memory = { check_max( 10.GB * task.attempt, 'memory') }
}
}
params {
// Defaults only, expecting to be overwritten
max_memory = 1024.GB
max_cpus = 200
max_time = 240.h
}