nextflow.config

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

// Prevent local Python libraries from conflicting with those in the container.
env { PYTHONNOUSERSITE = 1 }

manifest {
  name = 'trimming'
  author = 'Felix Thalen'
  homePage = 'https://github.com/fethalen/trimming'
  description = 'Quality control and trimming'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.04.1'
  version = '1.0.0'
}

params {
  // Mandatory arguments
  reads = null

  // Input/output options
  single_end = false
  output = "trimming_output"

  // Trimming
  trim_min_length = 55
  trim_quality = 20
  trim_adapter = null
  trim_phred64 = null
  trim_forward_leading = null
  trim_forward_trailing = null
  trim_reverse_leading = null
  trim_reverse_trailing = null
  trim_leading_cutoff = null
  trim_trailing_cutoff = null

  // QC
  qc_adapters = null

  // Coverage estimate
  genome_size = 2.5
  min_coverage = 15

  // Flow control
  skip_coverage = false
  skip_trimming = false
  skip_qc = false

  // Miscellaneous
  help = false
  version = false
}

profiles {
  conda {
    params.enable_conda = true
    process.conda = "$baseDir/environment.yml"
  }
  debug {
    process.beforeScript = 'echo $HOSTNAME'
  }
  docker {
    docker.enabled = true
    docker.fixOwnership = true
  }
  singularity {
    singularity.enabled = true
    singularity.autoMounts = true
  }
}