nextflow.config

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



// Global default params, used in configs
params {

  // Workflow flags
  // TODO nf-core: Specify your pipeline's command line flags
  genome = "ucsc_hg19"
  // enhancer = "input/regions/enhancer.bed"
  // promoter = "input/regions/promoter.bed"
  // other_regions = ""
  // promoter_enhancer_pair = "input/regions/promoter_enhancer_pair.txt"
  // promoter_gene_pair = "input/regions/promoter_gene_pair.txt"
  // vcf = "test_input/variants/test.vcf.gz"
  // vcf_index = "test_input/variants/test.vcf.gz.tbi"
  promoter_enhancer_distance_threshold = 1000000
  // phenocov = "input/samples/pheno_covar.txt"
  weights = "test_input/enhancer_promoter_distance_weight.csv"
  fdr_cutoff = 0.1
  fasta = "test_input/test.hg19.fa.gz"
  chrom_size = "test_input/hg19.chrom.sizes"
  outdir = './results'
  chunk_size = 100
  permutation_multiplier = 10
  motif_scan_threshold = 0.0001

  // Boilerplate options
  name = false
  email_on_fail = false
  plaintext_email = false
  monochrome_logs = false
  help = false
  ucsc_base = "./ucsc"
  ucscIgnore = false
  tracedir = "${params.outdir}/pipeline_info"
  awsqueue = false
  awsregion = 'eu-west-1'
  custom_config_version = 'master'
  custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
  hostnames = false
  config_profile_description = false
  config_profile_contact = false
  config_profile_url = false
}

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

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

// Load nf-core custom profiles from different Institutions
try {
  includeConfig "${params.custom_config_base}/nfcore_custom.config"
} catch (Exception e) {
  System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
}

profiles {
  awsbatch { includeConfig 'conf/awsbatch.config' }
  conda { process.conda = "$baseDir/environment.yml" }
  debug { process.beforeScript = 'echo $HOSTNAME' }
  docker { docker.enabled = true }
  singularity { singularity.enabled = true }
  test { includeConfig 'conf/test.config' }
  mail { includeConfig 'conf/mail.config' }
}

// 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)'


// Load uscs genome files
includeConfig 'conf/ucsc.config'

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

timeline {
  enabled = true
  file = "${params.tracedir}/execution_timeline.html"
}
report {
  enabled = true
  file = "${params.tracedir}/execution_report.html"
}
trace {
  enabled = true
  file = "${params.tracedir}/execution_trace.txt"
}
dag {
  enabled = true
  file = "${params.tracedir}/pipeline_dag.svg"
}

manifest {
  name = 'fuxialexander/marvel'
  author = 'Alexander Fu Xi'
  homePage = 'https://github.com/fuxialexander/marvel'
  description = 'Multigranular Analysis of Regulatory Variants on the Epigenomic Landscape'
  mainScript = 'main.nf'
  nextflowVersion = '>=20.04.1'
  version = '1.1dev'
}

// 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
    }
  }
}