utd_ganymede.config

//Profile config names for nf-core/configs
params {
  config_profile_description = 'University of Texas at Dallas HPC cluster profile provided by nf-core/configs'
  config_profile_contact = 'Edmund Miller(@emiller88)'
  config_profile_url = 'http://docs.oithpc.utdallas.edu/'
}

env {
    TMPDIR = "/home/$USER/scratch/tmp"
    SINGULARITY_CACHEDIR="/home/$USER/scratch/singularity"
}

singularity {
  enabled = true
  envWhitelist='SINGULARITY_BINDPATH,LD_LIBRARY_PATH'
  autoMounts = true
  cacheDir = "/home/$USER/scratch/singularity"
}

def membership = "groups".execute().text

def select_queue = { memory, cpu ->
    if (memory <= 32.GB && cpu <= 16 && membership.contains('genomics')) {
        return 'genomics,normal'
    }
    if (memory > 32.GB && memory <= 125.GB && cpu <= 12 && membership.contains('kim')) {
        return 'Kim,128s'
    }
    if (memory > 32.GB && memory <= 125.GB && cpu <= 16) {
        return '128s'
    }
    if (memory <= 250.GB && cpu <= 28) {
        return '256i,256h'
    }
}

// Submit up to 300 concurrent jobs
// pollInterval and queueStatInterval of every 5 minutes
// submitRateLimit of 20 per minute
executor {
    queueSize = 300
    pollInterval = '5 min'
    queueStatInterval = '5 min'
    submitRateLimit = '20 min'
}

process {
  beforeScript = 'module load singularity/3.2.1'
  executor = 'slurm'
  queue = { select_queue(task.memory, task.cpu) }

  withLabel:process_low {
    cpus = { check_max( 2 * task.attempt, 'cpus' ) }
    memory = { check_max( 12.GB * task.attempt, 'memory' ) }
    time = { check_max( 6.h * task.attempt, 'time' ) }
  }

  withLabel:process_medium {
    cpus = { check_max( 16 * task.attempt, 'cpus' ) }
    memory = { check_max( 31.GB * task.attempt, 'memory' ) }
    time = { check_max( 8.h * task.attempt, 'time' ) }
  }

  withLabel:process_high {
    cpus = { check_max( 12 * task.attempt, 'cpus' ) }
    memory = { check_max( 120.GB * task.attempt, 'memory' ) }
    time = { check_max( 16.h * task.attempt, 'time' ) }
  }
}

params {
  max_memory = 250.GB
  max_cpus = 28
  max_time = 96.h
}