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base.config
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/*
* -------------------------------------------------
* genome-annotation Nextflow base config file
* -------------------------------------------------
*/
process {
cpus = { 1 * task.attempt }
memory = { check_max( 8.GB * task.attempt, 'memory') }
time = { 1.h * task.attempt }
errorStrategy = { task.exitStatus in [143,137] ? 'retry' : 'finish' }
maxRetries = 1
maxErrors = '-1'
withLabel: short_running {
time = { check_max(4.h * task.attempt, 'time') }
memory = { check_max( 8.GB * task.attempt, 'memory') }
cpus = { 1 * task.attempt }
}
withLabel: medium_running {
time = { check_max(12.h * task.attempt, 'time') }
memory = { check_max( 8.GB * task.attempt, 'memory') }
cpus = { 1 * task.attempt }
}
withLabel: long_running {
time = { check_max(48.h * task.attempt, 'time') }
memory = { check_max( 16.GB * task.attempt, 'memory') }
cpus = { 1 * task.attempt }
}
withLabel: extra_long_running {
time = { check_max(120.h * task.attempt, 'time') }
memory = { check_max( 16.GB * task.attempt, 'memory') }
cpus = { 1 * task.attempt }
}
withName:repeatModel {
time = { check_max(120.h * task.attempt, 'time') }
cpus = 16
memory = { check_max(32.GB * task.attempt, 'memory') }
}
withName:repeatMask {
cpus = params.max_cpus
memory = { check_max(16.GB * task.attempt, 'memory') }
time = { check_max(120.h * task.attempt, 'time') }
}
withName:estMinimap {
cpus = params.max_cpus
memory = { check_max(32.GB * task.attempt, 'memory') }
time = { check_max(16.h * task.attempt,'time') }
}
withName:transPasaMinimap {
cpus = params.max_cpus
memory = { check_max(32.GB * task.attempt, 'memory') }
time = { check_max(16.h * task.attempt,'time') }
}
withName:rseqMinimapTrinity {
cpus = params.max_cpus
memory = { check_max(32.GB * task.attempt, 'memory') }
time = { check_max(16.h * task.attempt,'time') }
}
withName:protMakeDB {
cpus = { check_max(1 * task.attempt, 'cpus') }
memory = { check_max(8.GB * task.attempt, 'memory') }
time = { check_max(4.h * task.attempt,'time') }
}
withName:protDiamondx {
cpus = { check_max(4 * task.attempt,'cpus') }
memory = { check_max(16.GB * task.attempt, 'memory') }
time = { check_max(48.h * task.attempt, 'time') }
}
withName:protExonerate {
cpus = { check_max(8 * task.attempt, 'cpus') }
memory = { check_max(16.GB * task.attempt, 'memory') }
time = { check_max(12.h * task.attempt, 'time') }
}
withName:rseqTrim {
cpus = { check_max(8 * task.attempt, 'cpus') }
memory = { check_max(8.GB * task.attempt, 'memory') }
time = { check_max(4.h * task.attempt, 'time') }
}
withName:rseqMakeDB {
cpus = { check_max(8 * task.attempt, 'cpus') }
memory = { check_max(16.GB * task.attempt, 'memory') }
time = { check_max(8.h * task.attempt , 'time') }
}
withName:rseqMap {
cpus = { check_max(16 * task.attempt, 'cpus') }
memory = { check_max(16.GB * task.attempt, 'memory') }
time = { check_max(8.h * task.attempt, 'time') }
}
withName:rseqMergeBams {
cpus = { check_max(16 * task.attempt, 'cpus') }
memory = { check_max(120.GB * task.attempt, 'memory') }
time = { check_max(24.h * task.attempt, 'time') }
}
withName:rseqHints {
cpus = { check_max(2 * task.attempt, 'cpus') }
memory = { check_max(64.GB * task.attempt, 'memory') }
time = { check_max(48.h * task.attempt, 'time') }
}
withName:rseqTrinity {
cpus = params.max_cpus
memory = { check_max(120.GB * task.attempt, 'memory') }
time = { check_max(120.h * task.attempt, 'time') }
}
withName:transSeqclean {
cpus = { check_max(4 * task.attempt, 'cpus') }
memory = { check_max(16.GB * task.attempt, 'memory') }
time = { check_max(48.h * task.attempt, 'time') }
}
withName:transPasa {
cpus = { check_max(8 * task.attempt, 'cpus') }
memory = { check_max(8.GB * task.attempt, 'memory') }
time = { check_max(120.h * task.attempt, 'time') }
}
withName:trainAugustus {
cpus = { check_max(8 * task.attempt, 'cpus') }
memory = { check_max(8.GB * task.attempt, 'memory') }
time = { check_max(480.h * task.attempt, 'time') }
}
withName:predAugustus {
cpus = params.max_cpus
memory = { check_max(16.GB * task.attempt, 'memory') }
time = { check_max(48.h * task.attempt, 'time') }
}
}
params {
// Defaults only, expecting to be overwritten
max_memory = 120.GB
max_cpus = 16
max_time = 240.h
}