nextflow.config

/*
 * -----------------------------------------------------
 *  UCL-BLIC/rnaseq_variant_calling Nextflow config file
 * -----------------------------------------------------
 * Default config options for all environments.
 * Cluster-specific config options should be saved
 * in the conf folder and imported under a profile
 * name here.
 */

// Global default params, used in configs
params {

  // Pipeline Options
  genome = false
  forward_stranded = false
  reverse_stranded = false
  unstranded = false
  splicesites = false
  outdir = './results'
  saveReference = false
  saveTrimmed = false
  saveAlignedIntermediates = false
  singleEnd = false
  reads = "data/*{1,2}.fastq.gz"

  // Custom trimming options
  clip_r1 = 0
  clip_r2 = 0
  three_prime_clip_r1 = 0
  three_prime_clip_r2 = 0

  // Defaults
  sampleLevel = false
  clusterOptions = false
  maxMultiqcEmailFileSize = 25.MB
  readPaths = null
  tracedir = "${params.outdir}"
}

profiles {

  legion {
    includeConfig 'conf/legion.config'
  }
  myriad {
    includeConfig 'conf/myriad.config'
  }
}

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

timeline {
  enabled = true
  file = "${params.tracedir}/pipeline_info/rnaseq_variant_calling_timeline.html"
}
report {
  enabled = true
  file = "${params.tracedir}/pipeline_info/rnaseq_variant_calling_report.html"
}
trace {
  enabled = true
  file = "${params.tracedir}/pipeline_info/rnaseq_variant_calling_trace.txt"
}
dag {
  enabled = true
  file = "${params.tracedir}/pipeline_info/rnaseq_variant_calling_DAG.svg"
}

manifest {
  name = 'UCL-BLIC/rnaseq_variant_calling'
  description = 'Nextflow RNA-Seq variant calling pipeline.'
  homePage = 'https://github.com/UCL-BLICrnaseq_variant_calling'
  author = 'LC'
  version = '1.1'
  mainScript = 'main.nf'
  nextflowVersion = '>=0.32.0'
}

// 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
    }
  }
}