nci_gadi.config

// NCI Gadi nf-core configuration profile
params {
    config_profile_description = 'NCI Gadi HPC profile provided by nf-core/configs'
    config_profile_contact = 'Georgie Samaha (@georgiesamaha), Matthew Downton (@mattdton)'
    config_profile_url = 'https://opus.nci.org.au/display/Help/Gadi+User+Guide'
    project = System.getenv("PROJECT")
}

// Enable use of Singularity to run containers
singularity {
    enabled = true
    autoMounts = true
}

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

// Define process resource limits
process {
    executor = 'pbspro'
    project = System.getenv("PROJECT")
    storage = 'scratch/params.project'
    module = 'singularity'
    cache = 'lenient'
    stageInMode = 'symlink'
    queue = { task.memory < 128.GB ? 'normalbw' : (task.memory >= 128.GB && task.memory <= 190.GB ? 'normal' : (task.memory > 190.GB && task.memory <= 1020.GB ? 'hugemembw' : '')) }
    beforeScript = 'module load singularity'
}

// Write custom trace file with outputs required for SU calculation
def trace_timestamp = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss')
trace {
    enabled = true
    overwrite = false
    file = "./gadi-nf-core-trace-${trace_timestamp}.txt"
    fields = 'name,status,exit,duration,realtime,cpus,%cpu,memory,%mem,rss'
}