nextflow.config

// Global default params, used in configs
params {
  // SRA download options
  public_data_ids              = ''
  curl_max_time                = 600
  timeout_max_time             = '12h'

  // Boilerplate options
  outdir                       = './results'
  tracedir                     = "${params.outdir}/pipeline_info"
  publish_dir_mode             = 'copy'

  // Max resource options
  // Defaults only, expecting to be overwritten
  max_memory                   = '8.GB'
  max_cpus                     = 4
  max_time                     = '24.h'
}

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

// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'

profiles {
  docker {
    docker.enabled         = true
    // 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)'
    singularity.enabled    = false
    podman.enabled         = false
    shifter.enabled        = false
    charliecloud.enabled   = false
  }
  singularity {
    singularity.enabled    = true
    singularity.autoMounts = true
    docker.enabled         = false
    podman.enabled         = false
    shifter.enabled        = false
    charliecloud.enabled   = false
  }
  test  { includeConfig 'conf/test_sra.config' }
  crick { includeConfig 'conf/crick.config'    }
}

// Export these variables to prevent local Python/R libraries from conflicting with those in the container
env {
  PYTHONNOUSERSITE = 1
  R_PROFILE_USER   = "/.Rprofile"
  R_ENVIRON_USER   = "/.Renviron"
}

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

def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
  enabled = true
  file    = "${params.tracedir}/execution_timeline_${trace_timestamp}.html"
}
report {
  enabled = true
  file    = "${params.tracedir}/execution_report_${trace_timestamp}.html"
}
trace {
  enabled = true
  file    = "${params.tracedir}/execution_trace_${trace_timestamp}.txt"
}
dag {
  enabled = true
  file    = "${params.tracedir}/pipeline_dag_${trace_timestamp}.svg"
}

// 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
    }
  }
}