2022-03-12 10:47:33 +00:00
|
|
|
params {
|
2022-03-12 13:38:42 +00:00
|
|
|
config_profile_description = 'South Australian Health and Medical Research Institute (SAHMRI) HPC cluster profile.'
|
|
|
|
|
config_profile_contact = 'Nathan Watson-Haigh (nathan.watson-haigh@sahmri.com)'
|
|
|
|
|
config_profile_url = "https://sahmri.org.au"
|
2022-03-12 10:47:33 +00:00
|
|
|
max_memory = 375.GB
|
|
|
|
|
max_cpus = 32
|
|
|
|
|
max_time = 14.d
|
2022-03-15 01:11:51 +00:00
|
|
|
igenomes_base = '/cancer/storage/shared/igenomes/references/'
|
2022-03-12 10:47:33 +00:00
|
|
|
}
|
|
|
|
|
process {
|
|
|
|
|
executor = 'slurm'
|
|
|
|
|
queue = 'sahmri_prod_hpc,sahmri_cancer_hpc'
|
|
|
|
|
maxRetries = 2
|
|
|
|
|
|
|
|
|
|
cpus = { check_max( 2 * task.attempt, 'cpus') }
|
|
|
|
|
memory = { check_max( 1.GB * task.attempt, 'memory') }
|
|
|
|
|
time = { check_max( 10.m * task.attempt, 'time') }
|
|
|
|
|
}
|
|
|
|
|
executor {
|
|
|
|
|
queueSize = 50
|
|
|
|
|
submitRateLimit = '10 sec'
|
|
|
|
|
}
|
|
|
|
|
singularity {
|
|
|
|
|
enabled = true
|
|
|
|
|
autoMounts = true
|
2022-03-12 21:09:31 +00:00
|
|
|
beforeScript = 'export PATH=/apps/opt/singularity/latest/bin:${PATH}'
|
2022-03-12 10:47:33 +00:00
|
|
|
cacheDir = '/cancer/storage/shared/simg'
|
|
|
|
|
}
|
|
|
|
|
cleanup = true
|
