class MiGA::Cli::Action::PreprocWf

# File lib/miga/cli/action/preproc_wf.rb, line 11
def parse_cli
  default_opts_for_wf
  cli.defaults = { mytaxa: false }
  cli.parse do |opt|
    opt.on(
      '-i', '--input-type STRING',
      '(Mandatory) Type of input data, one of the following:',
      *MiGA::Cli::Action::Add.INPUT_TYPES.map{ |k,v| "~ #{k}: #{v[0]}" }
    ) { |v| cli[:input_type] = v.downcase.to_sym }
    opt.on(
      '-m', '--mytaxa_scan',
      'Perform MyTaxa scan analysis'
    ) { |v| cli[:mytaxa] = v }
    opts_for_wf(opt, 'Input files as defined by --input-type',
      multi: true, cleanup: false, ncbi: false)
  end
end

# File lib/miga/cli/action/preproc_wf.rb, line 29
def perform
  # Input data
  cli.ensure_par(input_type: '-i')
  p_metadata = Hash[
    %w[project_stats haai_distances aai_distances ani_distances clade_finding]
      .map { |i| ["run_#{i}", false] }
  ]
  d_metadata = { run_distances: false }
  unless cli[:mytaxa]
    d_metadata[:run_mytaxa_scan] = false
    d_metadata[:run_mytaxa] = false
  end
  p = create_project(cli[:input_type], p_metadata, d_metadata)
  # Run
  run_daemon
  summarize
end