class MiGA::Cli::Action::IndexWf

# File lib/miga/cli/action/index_wf.rb, line 10
def parse_cli
  default_opts_for_wf
  cli.defaults = { mytaxa: false }
  cli.parse do |opt|
    opt.on(
      '-m', '--mytaxa-scan',
      'Perform MyTaxa scan analysis'
    ) { |v| cli[:mytaxa] = v }
    opts_for_wf_distances(opt)
    opts_for_wf(
      opt, 'Input genome assemblies (nucleotides, FastA)',
      cleanup: false, project_type: true
    )
  end
end

# File lib/miga/cli/action/index_wf.rb, line 26
def perform
  # Input data
  p = create_project(:assembly, {}, run_mytaxa_scan: cli[:mytaxa])

  # Run
  run_daemon
  summarize
end