nf-configs/conf/sage.config

params {
  config_profile_description = 'The Sage Bionetworks profile'
  config_profile_contact = 'Bruno Grande (@BrunoGrandePhD)'
  config_profile_url = 'https://github.com/Sage-Bionetworks-Workflows'
}

process {

  cpus   = { check_max( 1    * slow(task.attempt), 'cpus'   ) }
  memory = { check_max( 6.GB * task.attempt,       'memory' ) }
  time   = { check_max( 24.h * task.attempt,       'time'   ) }

  errorStrategy = { task.exitStatus in [143,137,104,134,139,247] ? 'retry' : 'finish' }
  maxRetries    = 5
  maxErrors     = '-1'

  // Process-specific resource requirements
  withLabel:process_low {
    cpus   = { check_max( 4     * slow(task.attempt),  'cpus'   ) }
    memory = { check_max( 12.GB * task.attempt,        'memory' ) }
    time   = { check_max( 24.h  * task.attempt,        'time'   ) }
  }
  withLabel:process_medium {
    cpus   = { check_max( 12    * slow(task.attempt), 'cpus'   ) }
    memory = { check_max( 36.GB * task.attempt,       'memory' ) }
    time   = { check_max( 48.h  * task.attempt,       'time'   ) }
  }
  withLabel:process_high {
    cpus   = { check_max( 24    * slow(task.attempt), 'cpus'   ) }
    memory = { check_max( 72.GB * task.attempt,       'memory' ) }
    time   = { check_max( 96.h  * task.attempt,       'time'   ) }
  }
  withLabel:process_long {
    time   = { check_max( 192.h  * task.attempt,   'time'   ) }
  }
  withLabel:process_high_memory {
    memory = { check_max( 128.GB * task.attempt,   'memory' ) }
  }

  // Preventing Sarek labels from using the actual maximums
  withLabel:memory_max {
    memory = { check_max( 128.GB * task.attempt,   'memory' ) }
  }
  withLabel:cpus_max {
    cpus   = { check_max( 24    * slow(task.attempt), 'cpus'   ) }
  }

}

aws {
  region = "us-east-1"
}

params {
  igenomes_base = 's3://sage-igenomes/igenomes'
  max_memory    = 500.GB
  max_cpus      = 64
  max_time      = 168.h  // One week
}

// Function to slow the increase of the resource multipler
// as attempts are made. The rationale is that some CPUs
// don't need to be increased as fast as memory.
def slow(attempt, factor = 2) {
  return Math.ceil( attempt / factor) as int
}


// Function to ensure that resource requirements don't go
// beyond a maximum limit (copied here for Sarek v2)
def check_max(obj, type) {
    if (type == 'memory') {
        try {
            if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
                return params.max_memory as nextflow.util.MemoryUnit
            else
                return obj
        } catch (all) {
            println "   ### ERROR ###   Max memory '${params.max_memory}' is not valid! Using default value: $obj"
            return obj
        }
    } else if (type == 'time') {
        try {
            if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
                return params.max_time as nextflow.util.Duration
            else
                return obj
        } catch (all) {
            println "   ### ERROR ###   Max time '${params.max_time}' is not valid! Using default value: $obj"
            return obj
        }
    } else if (type == 'cpus') {
        try {
            return Math.min( obj, params.max_cpus as int )
        } catch (all) {
            println "   ### ERROR ###   Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
            return obj
        }
    }
}