pathogenflow/nextflow.config at main · Gagi1993/pathogenflow · GitHub

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params {
  concat_dir    = "data/concat"
  output_dir    = "results"
  kraken_db     = "${projectDir}/db/minikraken2_v2_8GB_201904_UPDATE"
  svevrste_file = "results/svevrste.txt"
  trim_dir      = "results/trim"   // <── Add for fastp outputs
  samplesheet = "samplesheet.csv"
  kma_entero_db = "${baseDir}/db/kma_db/entero_db"
  kma_entero_fasta = "${baseDir}/db/kma_db/entero_db.fasta"
  amrfinder_db = "${baseDir}/db/amr/amrfinder"
  rgi_db = "${baseDir}/db/amr/rgi"
  abricate_db = "db/abricate_db"
  refseq_masher_sketch = "${projectDir}/db/campy/refmash/campylobacter_ref.msh"

  // fastp defaults
  fastp_cut_front        = true   // -5
  fastp_cut_tail         = true   // -3
  fastp_cut_mean_quality = 20     // -M
  fastp_trim_front1      = 14     // -f
  fastp_trim_tail1       = 5      // -t
  fastp_trim_front2      = 14     // -F
  fastp_trim_tail2       = 5      // -T

  // KMA defualts
  kma_proxi = 0.9
  kma_md    = 50
  kma_mrs   = 0.3
  kma_mrc   = 0.6
  kma_bcd   = 10

  // bcftools mpileup defaults
  bcftools_max_depth       = 100000         // -d
  bcftools_max_idepth      = 10000000       // --max-idepth
  bcftools_min_bq          = 20             // -Q

  // bcftools consensus filter
  bcftools_min_dp          = 10             // for 'INFO/DP >= X'

  // spades
  spades_cov_cutoff = 8   // default; can be changed at runtime

  //amrfinder
  amrfinder_cov = 0.6
  amrfinder_ident = 0.9

  //abricate
  abricate_minid = 90
  abricate_mincov = 60

}


params.species_map = [
  '1352'     : "results/bacteria/efaecium/fastqconcat",    // Enterococcus faecium
  '1351'     : "results/bacteria/efaecalis/fastqconcat",   // Enterococcus faecalis
  '1637'     : "results/bacteria/listeria/fastqconcat",    // Listeria
  '590'      : "results/bacteria/salmonela/fastqconcat",   // Salmonella
  '1301'      : "results/bacteria/bhs/fastqconcat",         // Streptococcus
  '194'      : "results/bacteria/campy/fastqconcat",       // Campylobacter
  '1279'     : "results/bacteria/aureus/fastqconcat",      // Staphylococcus
  '561'      : "results/bacteria/ecoli/fastqconcat",       // Escherichia coli
  '445'      : "results/bacteria/legionela/fastqconcat",   // Legionella
  '482'      : "results/bacteria/neisseria/fastqconcat",   // Neisseria
  '570'      : "results/bacteria/klebsiele/fastqconcat",   // Klebsiella
  '517'      : "results/bacteria/bpert/fastqconcat",       // Bordetella
  '694002'   : "results/virus/covid/fastqconcat",          // Betacoronavirus
  '197911'   : "results/virus/flu/fastqconcat",            // Alphainfluenzavirus
  '197912'   : "results/virus/flu/fastqconcat",            // Betainfluenzavirus
  '12059'    : "results/virus/enterovirus/fastqconcat",    // Enterovirus
  '1868215'  : "results/virus/rsv/fastqconcat",            // Orthopneumovirus
  '11229'    : "results/virus/measles/fastqconcat",        // Morbillivirus
  'unknown'  : "results/unknown/fastqconcat"
]


process {
  cpus = 16
  memory = '25 GB'
  maxForks = 5
  time = '24h'
}


conda {
  enabled = true
  autoActivate = true
  mamba = true
}