params {
    config_profile_name        = 'Fred Hutch'
    config_profile_description = 'Fred Hutch Cancer Center HPC profile'
    config_profile_contact     = 'dgratz@fredhutch.org'
    config_profile_url         = 'https://sciwiki.fredhutch.org/'
    // Same as resourceLimits, but for older pipelines
    max_memory = 700.GB
    max_cpus = 36
    max_time = 720.h
    scratchDir = "${System.getenv('HOME')}/nextflow"
}
 
// If the user does not provide a scratch directory, use their home dir
workDir = params.scratchDir
 
process {
    executor = 'slurm'
    // clusterOptions = {} // If we want default slurm configs
    queue = { task.time > 12.h ? 'campus-new' : 'short' }
 
    maxRetries = 2
    errorStrategy = { task.exitStatus in [12,104,137,134,139,140,141,143,151,247] ? 'retry' : 'finish' }
 
    resourceLimits = [
        memory: 700.GB,
        cpus: 36,
        time: 720.h
    ]
    // Per the scicomp wiki, memory requests don't mean much on our system. Use CPUs as a proxy for mem requests
    // Request 1 CPU for each 4 GB of memory
    // https://sciwiki.fredhutch.org/scicomputing/compute_jobs/#memory
    cpus    = { 5 * task.attempt }
    memory  = { 20.GB * task.attempt }
    time    = { 24.h * task.attempt }
    withLabel:process_single {
        cpus   = { 2 * task.attempt }
        memory = { 8.GB * task.attempt }
        time   = { 12.h * task.attempt }
    }
    withLabel:process_low {
        cpus   = { 4 * task.attempt }
        memory = { 16.GB * task.attempt }
        time   = { 24.h  * task.attempt }
    }
    withLabel:process_medium {
        cpus   = { 16 * task.attempt }
        memory = { 56.GB * task.attempt }
        time   = { 72.h  * task.attempt }
    }
    withLabel:process_high {
        cpus   = 32
        memory = { 128.GB * task.attempt }
        time   = { 120.h  * task.attempt }
    }
    withLabel:process_long {
        cpus   = { 12 * task.attempt }
        memory = { 96.GB * task.attempt }
        time   = { 336.h  * task.attempt }
    }
}
 
executor {
    // How many jobs can be submitted at once
    queueSize = 16
    // Maximum jobs per second
    submitRateLimit = "10/1sec"
}
 
apptainer {
    enabled = true
    // Checks if TMPDIR is defined in the environment before mounting to avoid breaks
    runOptions = "--containall " + (System.getenv('TMPDIR') ? "-B \$TMPDIR" : "")
}
 
// clean the generated files in the working directory
// having this as true sometimes breaks things
cleanup = false