mirror of
https://github.com/MillironX/nf-configs.git
synced 2024-11-22 00:26:03 +00:00
57 lines
1.2 KiB
Text
57 lines
1.2 KiB
Text
/*
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
Sheffield Bioinformatics Core Configuration Profile - ShARC
|
|
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
|
|
Base Institutional Configuration
|
|
|
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
|
*/
|
|
|
|
|
|
params {
|
|
|
|
// nf-core specific parameters displayed in header summary of each run
|
|
|
|
config_profile_description = 'Sheffield Bioinformatics Core - ShARC'
|
|
config_profile_contact = 'Lewis Quayle (l.quayle@sheffield.ac.uk)'
|
|
config_profile_url = 'https://docs.hpc.shef.ac.uk/en/latest/sharc/index.html'
|
|
|
|
// hpc resource limits
|
|
|
|
max_cpus = 16
|
|
max_memory = 64.GB
|
|
max_time = 96.h
|
|
|
|
}
|
|
|
|
|
|
// container engine
|
|
|
|
singularity {
|
|
|
|
enabled = true
|
|
autoMounts = true
|
|
|
|
}
|
|
|
|
|
|
// hpc configuration specific to ShARC
|
|
|
|
process {
|
|
|
|
// scheduler
|
|
|
|
executor = 'sge'
|
|
penv = 'smp'
|
|
queue = { task.time <= 6.h ? 'shortint.q' : 'all.q' }
|
|
clusterOptions = { "-l rmem=${task.memory.toGiga()}G" }
|
|
|
|
// error and retry handling
|
|
|
|
errorStrategy = { task.exitStatus in [143,137,104,134,139,140] ? 'retry' : 'finish' }
|
|
maxRetries = 2
|
|
|
|
}
|