class MiGA::Cli::Action::ClassifyWf

# File lib/miga/cli/action/classify_wf.rb, line 10
def parse_cli
  default_opts_for_wf
  cli.defaults = {
    download: false, summaries: true, pvalue: 0.1,
    local: File.expand_path('.miga_db', ENV['MIGA_HOME'])
  }
  cli.parse do |opt|
    opt.on(
      '--download-db',
      'Attempt to download the reference database (all default options)',
      'It is recommended to use "miga get_db" separately instead'
    ) { |v| cli[:download] = v }
    opt.on(
      '-n', '--database STRING',
      'Name of the reference database to use',
      'By default, the first locally listed database is used'
    ) { |v| cli[:database] = v.to_sym }
    opt.on(
      '-p', '--p-value FLOAT', Float,
      'Maximum p-value to transfer taxonomy',
      "By default: #{cli[:pvalue]}"
    ) { |v| cli[:pvalue] = v }
    opt.on(
      '-l', '--local-dir PATH',
      "Local directory to store the database. By default: #{cli[:local]}"
    ) { |v| cli[:local] = v }
    opt.on(
      '--db-path STRING',
      'Path to the reference database to use, a fully indexed MiGA project',
      'If defined, --local-dir and --database are ignored'
    ) { |v| cli[:db_path] = v }
    opt.on(
      '--no-summaries',
      'Do not generate intermediate step summaries'
    ) { |v| cli[:summaries] = v }
    opts_for_wf(opt, 'Input genome assemblies (nucleotides, FastA)')
  end
end

# File lib/miga/cli/action/classify_wf.rb, line 49
def perform
  # Input data
  ref_db = reference_db
  norun = %w[
    haai_distances aai_distances ani_distances clade_finding
  ]
  p_metadata = Hash[norun.map { |i| ["run_#{i}", false] }]
  p = create_project(
    :assembly,
    p_metadata,
    run_mytaxa_scan: false, run_distances: false
  )
  p.set_option(:ref_project, ref_db.path)
  p.set_option(:tax_pvalue, cli[:pvalue])

  # Run
  run_daemon
  summarize(%w[cds assembly essential_genes]) if cli[:summaries]
  summarize(%w[taxonomy])
  unless cli[:prepare_and_exit]
    cli.say "Summary: classification"
    ofile = File.expand_path('classification.tsv', cli[:outdir])
    call_cli(['ls', '-P', cli[:outdir], '-m', 'tax', '--tab', '-o', ofile])
  end
  cleanup
end