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base.config
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/*
vim: syntax=groovy
-*- mode: groovy;-*-
* -------------------------------------------------
* Nextflow base config file
* -------------------------------------------------
* A 'blank slate' config file, appropriate for general
* use on most high performace compute environments.
* Assumes that all software is installed and available
* on the PATH. Runs in `local` mode - all jobs will be
* run on the logged in environment.
*/
process {
cpus = { check_max( 1 * task.attempt, 'cpus' ) }
memory = { check_max( 8.GB * task.attempt, 'memory' ) }
time = { check_max( 2.h * task.attempt, 'time' ) }
errorStrategy = { task.exitStatus == 143 ? 'retry' : 'finish' }
maxRetries = 1
maxErrors = '-1'
// Environment modules and resource requirements
$fastqc {
errorStrategy = { task.exitStatus == 143 ? 'retry' : 'ignore' }
}
$trim_galore {
cpus = { check_max( 2 * task.attempt, 'cpus' ) }
memory = { check_max( 16.GB * task.attempt, 'memory' ) }
time = { check_max( 8.h * task.attempt, 'time' ) }
}
$bwa{
cpus = { check_max( 8 * task.attempt, 'cpus' ) }
memory = { check_max( 64.GB * task.attempt, 'memory' ) }
time = { check_max( 24.h * task.attempt, 'time' ) }
}
$samtools {
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
memory = { check_max( 32.GB * task.attempt, 'memory' ) }
time = { check_max( 8.h * task.attempt, 'time' ) }
}
$bwa_mapped{
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
memory = { check_max( 32.GB * task.attempt, 'memory' ) }
time = { check_max( 8.h * task.attempt, 'time' ) }
errorStrategy = { task.exitStatus == 143 ? 'retry' : 'ignore' }
}
$picard {
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
memory = { check_max( 32.GB * task.attempt, 'memory' ) }
time = { check_max( 8.h * task.attempt, 'time' ) }
}
$countstat {
time = { check_max( 8.h * task.attempt, 'time' ) }
errorStrategy = { task.exitStatus == 143 ? 'retry' : 'ignore' }
}
$phantompeakqualtools {
time = { check_max( 8.h * task.attempt, 'time' ) }
errorStrategy = { task.exitStatus == 143 ? 'retry' : 'ignore' }
}
$calculateNSCRSC {
errorStrategy = { task.exitStatus == 143 ? 'retry' : 'ignore' }
}
$deepTools {
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
memory = { check_max( 32.GB * task.attempt, 'memory' ) }
time = { check_max( 8.h * task.attempt, 'time' ) }
errorStrategy = { task.exitStatus == 143 ? 'retry' : 'ignore' }
}
$ngsplot {
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
memory = { check_max( 32.GB * task.attempt, 'memory' ) }
time = { check_max( 8.h * task.attempt, 'time' ) }
errorStrategy = { task.exitStatus == 143 ? 'retry' : 'ignore' }
}
$macs {
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
memory = { check_max( 32.GB * task.attempt, 'memory' ) }
time = { check_max( 8.h * task.attempt, 'time' ) }
}
$saturation {
cpus = { check_max( 4 * task.attempt, 'cpus' ) }
memory = { check_max( 32.GB * task.attempt, 'memory' ) }
time = { check_max( 8.h * task.attempt, 'time' ) }
}
$saturation_r {
errorStrategy = { task.exitStatus == 143 ? 'retry' : 'ignore' }
}
$chippeakanno {
errorStrategy = { task.exitStatus == 143 ? 'retry' : 'ignore' }
}
$get_software_versions {
memory = { check_max( 2.GB * task.attempt, 'memory' ) }
executor = 'local'
errorStrategy = 'ignore'
}
$multiqc {
memory = { check_max( 2.GB * task.attempt, 'memory' ) }
executor = 'local'
errorStrategy = { task.exitStatus == 143 ? 'retry' : 'ignore' }
}
}
params {
// Defaults only, expecting to be overwritten
max_memory = 128.GB
max_cpus = 16
max_time = 240.h
}