rosalind_uge.config

/*
* ---------------------------------------------------------
*       nf-core/configs: Rosalind UGE config
* ---------------------------------------------------------
*/


// Basic params of config file
params {
    config_profile_description = 'Rosalind UGE config file'
    config_profile_contact     = 'Gregory Sprenger (@gregorysprenger)'
}

// Use Singularity
singularity {
    enabled    = true
    autoMounts = true
}

// Submit up to 100 jobs at once with 15 secs between to avoid spamming the cluster
executor {
    queueSize    = 100
    pollInterval = '15 sec'
}

// Process specific resource requirements
process {
    // Error and retry handling
    errorStrategy  = { task.exitStatus in [143, 137, 104, 134, 139, 71, 255] ? 'retry' : 'finish' }
    maxRetries     = 3

    // Executor and queue information
    executor       = 'sge'
    penv           = 'smp'
    queue          = { task.time <= 4.h ? 'short.q' : task.time > 5.h ? 'all.q' : 'short.q' }
    clusterOptions = { "-l h_vmem=${task.memory.toString().replaceAll(/[\sB]/, '')}" }
}