nextflow.config

/*
 * -------------------------------------------------
 *  NanoRTax Nextflow config file
 * -------------------------------------------------
 * Default config options for all environments.
 */

// Global default params, used in configs
params {

  // Workflow flags
  reads = ""
  outdir = './results'
  min_read_length = 1400
  max_read_length = 1700
  taxonkit_db = "db/"
  blast_db = "db/16S_ribosomal_RNA"
  blast_taxdb = "db/taxdb"
  kraken_db = "db/16S_RDP_k2db"
  centrifuge_db = "db/silva"
  cntrf_min_hitlen = 16
  blast_evalue = 11
  blast_max_hsps = 50

  // Boilerplate options
  name = false
  help = false
  monochrome_logs = false
  
  // Defaults only, expecting to be overwritten
  max_memory = 128.GB
  max_cpus = 16
  max_time = 240.h

}

// Container slug. Stable releases should specify release tag!
// Developmental code should specify :dev
process.container = 'hecrp/nanortax:latest'

// Load base.config by default for all pipelines
includeConfig 'conf/base.config'

profiles {
  conda { 
    conda.enabled = true
    process.conda = "$baseDir/environment.yml" }
  debug { process.beforeScript = 'echo $HOSTNAME' }
  docker {
    docker.enabled = true
    docker.temp = "$baseDir"
    // Avoid this error:
    //   WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
    // Testing this in nf-core after discussion here https://github.com/nf-core/tools/pull/351
    // once this is established and works well, nextflow might implement this behavior as new default.
    docker.runOptions = '-u $(id -u):$(id -g)'
    docker.fixOwnership = true
  }
  singularity {
    singularity.enabled = true
    singularity.autoMounts = true
  }
  test { includeConfig 'conf/test.config' }
}

// Export this variable to prevent local Python libraries from conflicting with those in the container
env {
  PYTHONNOUSERSITE = 1
}

// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']

manifest {
  name = 'NanoRTax'
  author = 'Laura Ciuffreda, Héctor Rodríguez Pérez'
  homePage = 'https://github.com/genomicsiter/nanortax'
  description = 'Real-time analysis pipeline for nanopore metagenomic data'
  mainScript = 'main.nf'
  nextflowVersion = '>=19.10.0'
  version = '1.0dev'
}

// Function to ensure that resource requirements don't go beyond
// a maximum limit
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
    }
  }
}