config.yaml

db_dir: "databases" # relative to workflow base or absolute
search:
  # NOTE: with custom databases make sure to set: taxonlist: ""  (empty string)
  db: "rvdb80.dmnd"
  taxonlist: "--taxonlist 2732396,2731342" # screen only for Orthornaviridae and Monodnaviridae
  # taxonlist: "" <<< use with custom dbs that haven't been built with a diamond taxonomy !
  evalue: 1e-4
  min_length_nt: 250
  # expert
  other_args: "-c1 -b6 -F15 --sensitive --max-hsps 100 --range-culling -k 20 --outfmt 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore stitle"
  # devel - sensitivity adjustments for <40% identity - see diamond options - negatively affects speed
  # other_args: "-c1 -b6 -F15 --ultra-sensitive --range-culling -k 20 --outfmt 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore stitle"
  chop_window: 60000
  chop_step: 50000

retrosearch:
  db: "uniref50.dmnd"
  evalue: 1e-4
  # expert
  other_args: "-c1 -b6 -F15 --sensitive --max-hsps 100 --range-culling -k 20 --outfmt 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore stitle"
  # devel - only retro against Anopheles
  # other_args: "--taxonlist 7164 -c1 -b6 -F15 --range-culling -k 20 --outfmt 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore stitle"
  # devel - sensitivity adjustments for <40% identity - see diamond options - negatively affects speed 
  # other_args: "-c1 -b6 -F15 --ultra-sensitive --range-culling -k 20 --outfmt 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore stitle"

mask:
  # set to "" to disable masking
  # rest same as `search` above
  db: "mask.dmnd"
  
validate:
  # Options
  #   -b --min-bitscore-frac=<0:1>  Minimum bitscore relative to top hit per locus 
  #                                 to include hit in validation [default: 0.5]
  #   -E --eve-score-high=<0:100>   Minimum eve-score for high-confidence validatEVEs
  #                                 [default: 30]
  #   -e --eve-score-low=<0:100>    Minimum eve-score for low-confidence validatEVEs
  #                                 [default: 10]
  #   -r --retro-score-low=<0:100>  Minimum retro-score for low-confidence validatEVEs
  #                                 even if with high eve-score [default: 10]
  #   -m --maybe-score-frac=<0:1>   Relative weight of maybe-viral hints in eve-score
  #                                 computation [default: 0.2]
  # Example for stricter search, 75% of top-bitscore, minimum eve-score of 50
  # args: "-b 0.75 -E 50"
  args: ""