nf-configs/conf/uppmax.config

//Profile config names for nf-core/configs
params {
  config_profile_description = 'Swedish UPPMAX cluster profile provided by nf-core/configs.'
  config_profile_contact = 'Phil Ewels (@ewels)'
  config_profile_url = 'https://www.uppmax.uu.se/'
}

singularity {
  enabled = true
}

def hostname = "sinfo --local -N -h | head -1 | cut -f1 -d' ' ".execute().text.trim()

process {
  // closure to create a suitable clusterOptions
  def clusterOptionsCreator = { m ->
                            String base = "-A $params.project ${params.clusterOptions ?: ''}"
			    // Do not use -p node on irma or if a thin node/core is enough
			    if (m < 125.GB || hostname ==~ "i.*") {
			      return base
			    }
			    if (m < 250.GB) {
			      return base + " -p node -C mem256GB "
			    }
			    // Remaining cases use the largest available node (1 Tbyte for rackham, 512 Gbyte for others)
			    if (hostname ==~ "r.*") {
			      return base + " -p node -C mem1TB "
			    }
			    return base + " -p node -C mem512GB "
			  }


  executor = 'slurm'
  clusterOptions = { clusterOptionsCreator(task.memory) }
}

params {
  save_reference = true

  max_memory = 970.GB
  max_cpus = 16
  max_time = 240.h
  // illumina iGenomes reference file paths on UPPMAX
  igenomes_base = '/sw/data/uppnex/igenomes/'
}

if (hostname ==~ "b.*") {
  params.max_memory = 500.GB
}

if (hostname ==~ "s.*") {
  params.max_memory = 500.GB
  params.max_time = 700.h
}

if (hostname ==~ "i.*") {
  params.max_memory = 250.GB
}

if (hostname ==~ "r.*") {
  params.max_cpus = 20
}

profiles {
  devel {
    params {
      config_profile_description = 'Testing & development profile for UPPMAX, provided by nf-core/configs.'
      // Max resources to be requested by a devel job
      max_memory = 120.GB
      max_time = 1.h
    }
    executor.queueSize = 1
    process.queue = 'devel'
  }
}