nf-configs/conf/sahmri.config

params {
  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"
  max_memory      = 375.GB
  max_cpus        = 32
  max_time        = 14.d
  igenomes_base   = '/cancer/storage/shared/igenomes/references/'
}
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
  beforeScript    = 'export PATH=/apps/opt/singularity/latest/bin:${PATH}'
  cacheDir        = '/cancer/storage/shared/simg'
}
cleanup = true
profiles {
  debug {
    cleanup = false
  }
}