proteomicsTMT/nextflow.config at main · jpfeuffer/proteomicsTMT · GitHub

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// Global default params, used in configs
params {

  // Nf-core lint required params that are unused
  input = 'foobarbaz'

  // Workflow flags
  input = '' // the sdrf and spectra parameters are inferred from this one
  root_folder = ''
  local_input_type = ''
  database = ''
  expdesign = ''

  // Tools flags
  posterior_probabilities = 'percolator'
  add_decoys = false
  search_engines = 'comet'
  protein_inference = 'aggregation'
  psm_pep_fdr_cutoff = 0.10
  protein_level_fdr_cutoff = 0.05

  // decoys
  decoy_affix = 'DECOY_'
  affix_type = 'prefix'

  // peak picking if used
  openms_peakpicking = false
  peakpicking_inmemory = false
  peakpicking_ms_levels = '' // means all/auto
  pp_debug = 0


  //Isobaric analyze
  isobaric_analyzer = true
  min_precursor_intensity = 1.0
  normalization = false
  isotope_correction = true
  iso_normalization = false
  min_reporter_intensity = 0.0
  min_precursor_purity = 0.0
  precursor_isotope_deviation = 10.0
  iso_debug = 1

  // shared search engine parameters
  enzyme = 'Trypsin'
  num_enzyme_termini = 'fully'
  allowed_missed_cleavages = 2
  precursor_mass_tolerance = 5
  precursor_mass_tolerance_unit = 'ppm'
  fixed_mods = 'Carbamidomethyl (C)'
  variable_mods = 'Oxidation (M)'
  isotope_error_range = '0,1'
  instrument = '' //auto-determined from tolerances
  protocol = 'automatic'
  min_precursor_charge = 2
  max_precursor_charge = 4
  min_peptide_length = 6
  max_peptide_length = 40
  num_hits = 1
  max_mods = 3
  db_debug = 0

  // PeptideIndexer flags
  IL_equivalent = true
  allow_unmatched = false

  // Percolator flags
  train_FDR = 0.05
  test_FDR = 0.05
  FDR_level = 'peptide-level-fdrs'
  klammer = false
  description_correct_features = 0
  subset_max_train = 300000

  // IDFilter
 psm_pep_fdr_cutoff = 0.05
 protgroup_score_cutoff = 0.0

  //IDMapper
  rt_tolerance = 5.0
  mz_tolerance = 20
  mz_measure = 'ppm'
  mz_reference = 'peptide'

  //FileMerger
  annotate_file_origin = false
  append_method = 'append_rows'

  //Epifany
  protein_fdr = false
  greedy_group_resolution = 'none'
  top_PSMs = 1

  //IDConflictResolver
  res_between_fet = 'off'

  //ProteinQuantifier
  top = 3
  average = 'median'
  best_charge_and_fraction = false
  normalize = false
  ratios = false
  fix_peptides = false


  // Defaults only, expecting to be overwritten
  max_memory = 128.GB
  max_cpus = 16
  max_time = 240.h

}
// 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']
includeConfig './base.config'

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
    }
  }
}