mirror of
https://github.com/MillironX/nf-configs.git
synced 2024-11-24 17:19:54 +00:00
50 lines
1.2 KiB
Text
50 lines
1.2 KiB
Text
//Profile config names for nf-core/configs
|
|
params {
|
|
config_profile_description = 'University of Edinburgh (eddie) cluster profile provided by nf-core/configs.'
|
|
config_profile_contact = 'Alison Meynert (@ameynert)'
|
|
config_profile_url = 'https://www.ed.ac.uk/information-services/research-support/research-computing/ecdf/high-performance-computing'
|
|
}
|
|
|
|
executor {
|
|
name = "sge"
|
|
queueSize = "100"
|
|
}
|
|
|
|
process {
|
|
clusterOptions = { task.memory ? "-l h_vmem=${task.memory.bytes/task.cpus}" : null }
|
|
scratch = true
|
|
penv = { task.cpus > 1 ? "sharedmem" : null }
|
|
|
|
// common SGE error statuses
|
|
errorStrategy = {task.exitStatus in [143,137,104,134,139,140] ? 'retry' : 'finish'}
|
|
maxErrors = '-1'
|
|
maxRetries = 3
|
|
|
|
beforeScript =
|
|
"""
|
|
. /etc/profile.d/modules.sh
|
|
module load 'roslin/singularity/3.5.3'
|
|
export SINGULARITY_TMPDIR="\$TMPDIR"
|
|
"""
|
|
}
|
|
|
|
params {
|
|
saveReference = true
|
|
// iGenomes reference base
|
|
igenomes_base = '/exports/igmm/eddie/BioinformaticsResources/igenomes'
|
|
max_memory = 384.GB
|
|
max_cpus = 32
|
|
max_time = 240.h
|
|
}
|
|
|
|
env {
|
|
MALLOC_ARENA_MAX=1
|
|
}
|
|
|
|
singularity {
|
|
envWhitelist = "SINGULARITY_TMPDIR,TMPDIR"
|
|
runOptions = '-p -B "$TMPDIR"'
|
|
enabled = true
|
|
autoMounts = true
|
|
}
|
|
|