Class: MiGA::Cli::Action::QualityWf

Inherits:
MiGA::Cli::Action show all
Includes:
Wf
Defined in:
lib/miga/cli/action/quality_wf.rb

Constant Summary

Constants included from MiGA

MiGA::CITATION, VERSION, VERSION_DATE, VERSION_NAME

Instance Attribute Summary

Attributes inherited from MiGA::Cli::Action

#cli

Attributes included from MiGA::Common::Net

#remote_connection_uri

Instance Method Summary collapse

Methods included from Wf

#call_cli, #cleanup, #create_project, #default_opts_for_wf, #download_datasets, #import_datasets, #initialize_empty_project, #opts_for_wf, #opts_for_wf_distances, #run_daemon, #summarize, #transfer_metadata

Methods inherited from MiGA::Cli::Action

#complete, #empty_action, #initialize, #launch, load, #name

Methods inherited from MiGA

CITATION, CITATION_ARRAY, DEBUG, DEBUG_OFF, DEBUG_ON, DEBUG_TRACE_OFF, DEBUG_TRACE_ON, FULL_VERSION, LONG_VERSION, VERSION, VERSION_DATE, #advance, debug?, debug_trace?, initialized?, #like_io?, #num_suffix, rc_path, #result_files_exist?, #say

Methods included from MiGA::Common::Path

#root_path, #script_path

Methods included from MiGA::Common::Format

#clean_fasta_file, #seqs_length, #tabulate

Methods included from MiGA::Common::Net

#download_file_ftp, #http_request, #known_hosts, #main_server, #net_method, #normalize_encoding, #remote_connection

Methods included from MiGA::Common::SystemCall

#run_cmd, #run_cmd_opts

Constructor Details

This class inherits a constructor from MiGA::Cli::Action

Instance Method Details

#parse_cli ⇒ Object 



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# File 'lib/miga/cli/action/quality_wf.rb', line 10

def parse_cli
  default_opts_for_wf
  cli.defaults = { mytaxa: false, min_qual: 'no' }
  cli.parse do |opt|
    opt.on(
      '-m', '--mytaxa-scan',
      'Perform MyTaxa scan analysis'
    ) { |v| cli[:mytaxa] = v }
    opts_for_wf(opt, 'Input genome assemblies (nucleotides, FastA)')
  end
end

#perform ⇒ Object 



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# File 'lib/miga/cli/action/quality_wf.rb', line 22

def perform
  # Input data
  norun = %w[
    project_stats haai_distances aai_distances ani_distances clade_finding
  ]
  p_metadata = Hash[norun.map { |i| ["run_#{i}", false] }]
  d_metadata = { run_distances: false }
  d_metadata[:run_mytaxa_scan] = false unless cli[:mytaxa]
  p = create_project(:assembly, p_metadata, d_metadata)

  # Run
  run_daemon
  summarize
  if cli[:mytaxa] && !cli[:prepare_and_exit]
    dir = File.expand_path('mytaxa_scan', cli[:outdir])
    Dir.mkdir(dir)
    p.each_dataset do |d|
      r = d.result(:mytaxa_scan) or next
      f = r.file_path(:report) or next
      FileUtils.cp(f, dir)
    end
  end
  cleanup
end