xanadu.config

params {
    config_profile_description = 'The UConn HPC profile'
    config_profile_contact     = 'noah.reid@uconn.edu'
    config_profile_url         = 'https://bioinformatics.uconn.edu/'

    // max resources
    max_memory                 = 2.TB
    max_cpus                   = 64
    max_time                   = 21.d

    // Path to shared singularity images
    singularity_cache_dir      = '/isg/shared/databases/nfx_singularity_cache'

}

process {
    executor                   = 'slurm'
    queue                      = { task.memory <= 245.GB ? 'general' : ( task.memory <= 512.GB ? 'himem' : 'himem2' ) }

    clusterOptions             = { [
        task.memory <= 245.GB ? '--qos=general' : '--qos=himem',
        // provide hardware constraints for particular processes
        //"${task.process.tokenize(':')[-1]}" ==~ /[BWAbwa]{3}[-_][MEme]{3}2.*/ ? '--constraint="AVX|AVX2|AVX512|SSE41|SSE42"' : ''
    ].join(' ').trim() }
}

executor {
    name                       = 'slurm'
    submitRateLimit            = '2 sec'
    queueSize                  = 100
}

singularity {
    enabled                    = true
    cacheDir                   = params.singularity_cache_dir
    autoMounts                 = true
    conda.enabled              = false
}