Module: MiGA::Cli::Action::Wf

Included in:
ClassifyWf, DerepWf, IndexWf, PreprocWf, QualityWf
Defined in:
lib/miga/cli/action/wf.rb

Overview

Helper module for workflows

Instance Method Summary collapse

Instance Method Details

#call_cli(cmd) ⇒ Object 



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# File 'lib/miga/cli/action/wf.rb', line 250

def call_cli(cmd)
  cmd << '-v' if cli[:verbose]
  MiGA::MiGA.DEBUG "Cli::Action::Wf.call_cli #{cmd}"
  MiGA::Cli.new(cmd.map(&:to_s)).launch(true)
end

#cleanup ⇒ Object 



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# File 'lib/miga/cli/action/wf.rb', line 240

def cleanup
  return if cli[:prepare_and_exit]
  return unless cli[:clean]

  cli.say 'Cleaning up intermediate files'
  %w[data daemon metadata miga.project.json].each do |f|
    FileUtils.rm_rf(File.expand_path(f, cli[:outdir]))
  end
end

#create_project(stage, p_metadata = {}, d_metadata = {}) ⇒ Object 



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# File 'lib/miga/cli/action/wf.rb', line 149

def create_project(stage, p_metadata = {}, d_metadata = {})
  cli.ensure_par(
    outdir: '-o',
    project_type: '--project-type',
    dataset_type: '--dataset-type'
  )
  paired = cli[:input_type].to_s.include?('_paired')
  cli[:regexp] ||= MiGA::Cli.FILE_REGEXP(paired)

  # Create empty project and populate with datasets
  p = initialize_empty_project(p_metadata)
  download_datasets
  import_datasets(stage)

  # Define datasets metadata
  p.load
  d_metadata[:type] = cli[:dataset_type]
  p.each_dataset { |d| transfer_metadata(d, d_metadata) }
  p
end

#default_opts_for_wf ⇒ Object 



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# File 'lib/miga/cli/action/wf.rb', line 7

def default_opts_for_wf
  cli.expect_files = true
  cli.defaults = {
    clean: false, project_type: :genomes, dataset_type: :popgenome,
    ncbi_draft: true, ncbi_ref: false,
    min_qual: MiGA::Project.OPTIONS[:min_qual][:default],
    prepare_and_exit: false
  }
end

#download_datasets ⇒ Object 



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# File 'lib/miga/cli/action/wf.rb', line 185

def download_datasets
  # Download datasets from NCBI
  unless cli[:ncbi_taxon].nil?
    what = cli[:ncbi_ref] ? '--reference' :
           cli[:ncbi_draft] ? '--all' : '--complete'
    cmd = ['ncbi_get', '-P', cli[:outdir], '-T', cli[:ncbi_taxon], what]
    cmd += ['--max', cli[:max_download]] if cli[:max_download]
    call_cli(cmd)
  end

  # Download datasets from GTDB
  unless cli[:gtdb_taxon].nil?
    cmd = ['gtdb_get', '-P', cli[:outdir], '-T', cli[:gtdb_taxon]]
    cmd << '--reference' if cli[:gtdb_ref]
    cmd += ['--max', cli[:max_download]] if cli[:max_download]
    call_cli(cmd)
  end

  # Download datasets from SeqCode Registry
  if cli[:seqcode_type]
    cmd = ['seqcode_get', '-P', cli[:outdir]]
    cmd += ['--max', cli[:max_download]] if cli[:max_download]
    call_cli(cmd)
  end
end

#import_datasets(stage) ⇒ Object 



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# File 'lib/miga/cli/action/wf.rb', line 211

def import_datasets(stage)
  call_cli(
    [
      'add',
      '--ignore-dups',
      '-P', cli[:outdir],
      '-t', cli[:dataset_type],
      '-i', stage,
      '-R', cli[:regexp]
    ] + cli.files
  ) unless cli.files.empty?
end

#initialize_empty_project(metadata) ⇒ Object 



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# File 'lib/miga/cli/action/wf.rb', line 170

def initialize_empty_project(metadata)
  call_cli(
    ['new', '-P', cli[:outdir], '-t', cli[:project_type]]
  ) unless MiGA::Project.exist? cli[:outdir]

  # Define project metadata
  p = cli.load_project(:outdir, '-o')
  metadata[:type] = cli[:project_type]
  transfer_metadata(p, metadata)
  %i[haai_p aai_p ani_p ess_coll min_qual].each do |i|
    p.set_option(i, cli[i])
  end
  p
end

#opts_for_wf(opt, files_desc, params = {}) ⇒ Object 



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# File 'lib/miga/cli/action/wf.rb', line 17

def opts_for_wf(opt, files_desc, params = {})
  {
    multi: false, cleanup: true, project_type: false, ncbi: true, qual: true
  }.each { |k, v| params[k] = v if params[k].nil? }
  opt.on(
    '-o', '--out_dir PATH',
    '(Mandatory) Directory to be created with all output data'
  ) { |v| cli[:outdir] = v }
  opt.on(
    '-P', '--project PATH',
    '::HIDE::' # Applying the principle of least surprise, alias of -o
  ) { |v| cli[:outdir] = v }
  opt.separator ''
  opt.separator "    FILES...: #{files_desc}"
  opt.separator ''
  opt.separator 'Workflow Control Options'
  opt.on(
    '-C', '--collection STRING',
    'Collection of essential genes to use as reference',
    'One of: dupont_2012 (default), lee_2019'
  ) { |v| cli[:ess_coll] = v }
  if params[:ncbi]
    opt.on(
      '-T', '--ncbi-taxon STRING',
      'Download all the genomes in NCBI classified as this taxon'
    ) { |v| cli[:ncbi_taxon] = v }
    opt.on(
      '--no-draft', '::HIDE::' # Deprecated
    ) { |v| cli[:ncbi_draft] = v }
    opt.on(
      '--ncbi-complete',
      'Only download complete genomes, not drafts (requires -T)'
    ) { |v| cli[:ncbi_draft] = !v }
    opt.on(
      '--ncbi-ref',
      'Only download RefSeq reference genomes (requires -T)'
    ) { |v| cli[:ncbi_ref] = v }
    opt.on(
      '-G', '--gtdb-taxon STRING',
      'Download all the genomes in GTDB classified as this taxon'
    ) { |v| cli[:gtdb_taxon] = v }
    opt.on(
      '--gtdb-ref',
      'Only download reference anchor genomes in GTDB (requires -G)'
    ) { |v| cli[:gtdb_ref] = v }
    opt.on(
      '-S', '--seqcode-type',
      'Download all type genomes from the SeqCode Registry'
    ) { |v| cli[:seqcode_type] = v }
    opt.on(
      '--max-download INT', Integer,
      'Maximum number of genomes to download (by default: unlimited)',
      'It applies independently to -T, -G and --S'
    ) { |v| cli[:max_download] = v }
  end
  if params[:qual]
    opt.on(
      '--min-qual FLOAT',
      'Minimum genome quality to include in analysis',
      "By default: #{cli[:min_qual]}"
    ) { |v| cli[:min_qual] = v == 'no' ? v : v.to_f }
  end
  if params[:cleanup]
    opt.on(
      '-c', '--clean',
      'Clean all intermediate files after generating the reports'
    ) { |v| cli[:clean] = v }
  end
  opt.on(
    '-R', '--name-regexp REGEXP', Regexp,
    'Regular expression indicating how to extract the name from the path',
    "By default: '#{MiGA::Cli.FILE_REGEXP}'"
  ) { |v| cli[:regexp] = v }
  opt_object_type(opt, :dataset, params[:multi])
  opt_object_type(opt, :project, params[:multi]) if params[:project_type]
  opt.on(
    '--daemon PATH',
    'Use custom daemon configuration in JSON format',
    'By default: ~/.miga_daemon.json'
  ) { |v| cli[:daemon_json] = v }
  opt.on(
    '-j', '--jobs INT', Integer,
    'Number of parallel jobs to execute',
    'By default controlled by the daemon configuration (maxjobs)'
  ) { |v| cli[:jobs] = v }
  opt.on(
    '-t', '--threads INT', Integer,
    'Number of CPUs to use per job',
    'By default controlled by the daemon configuration (ppn)'
  ) { |v| cli[:threads] = v }
  opt.on(
    '--threads-project INT', Integer,
    'Number of CPUs to use per project-wide job',
    'By default controlled by the daemon configuration (ppn_project or ppn)'
  ) { |v| cli[:threads_project] = v }
  opt.on(
    '--prepare-and-exit',
    'Create project and import datasets, but do not run any analyses'
  ) { |v| cli[:prepare_and_exit] = v }
end

#opts_for_wf_distances(opt) ⇒ Object 



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# File 'lib/miga/cli/action/wf.rb', line 118

def opts_for_wf_distances(opt)
  opt.on('--sensitive', 'Alias to: --aai-p blast+ --ani-p blast+') do
    cli[:aai_p] = 'blast+'
    cli[:ani_p] = 'blast+'
  end
  opt.on('--fast', 'Alias to: --aai-p diamond --ani-p fastani (default)') do
    cli[:aai_p] = 'diamond'
    cli[:ani_p] = 'fastani'
  end
  opt.on(
    '--only-ani', 'Alias to: --haai-p no --aai-p no',
    'Use only for collections with expected AAI around or above 85%'
  ) do
    cli[:haai_p] = 'no'
    cli[:aai_p] = 'no'
  end
  opt.on(
    '--haai-p STRING',
    'hAAI search engine. One of: blast+, fastaai, blat, diamond, fastaai, no',
    'The default is "no" for clade projects and "fastaai" otherwise'
  ) { |v| cli[:haai_p] = v }
  opt.on(
    '--aai-p STRING',
    'AAI search engine. One of: blast+, blat, diamond (default), no'
  ) { |v| cli[:aai_p] = v }
  opt.on(
    '--ani-p STRING',
    'ANI search engine. One of: blast+, blat, fastani (default)'
  ) { |v| cli[:ani_p] = v }
end

#run_daemon ⇒ Object 



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# File 'lib/miga/cli/action/wf.rb', line 256

def run_daemon
  return if cli[:prepare_and_exit]

  cmd  = ['daemon', 'run', '-P', cli[:outdir], '--shutdown-when-done']
  cmd += ['--json', cli[:daemon_json]] if cli[:daemon_json]
  cmd += ['--max-jobs', cli[:jobs]] if cli[:jobs]
  cmd += ['--ppn', cli[:threads]] if cli[:threads]
  cmd += ['--ppn-project', cli[:threads_project]] if cli[:threads_project]
  cmd += ['--debug', MiGA::MiGA.debug_trace? ? '2' : '1'] if MiGA::MiGA.debug?
  cwd = Dir.pwd
  call_cli(cmd)
  Dir.chdir(cwd)
end

#summarize(which = %w[cds assembly essential_genes ssu])) ⇒ Object 



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# File 'lib/miga/cli/action/wf.rb', line 224

def summarize(which = %w[cds assembly essential_genes ssu])
  return if cli[:prepare_and_exit]

  which.each do |r|
    cli.say "Summary: #{r}"
    call_cli(
      [
        'summary',
        '-P', cli[:outdir], '-r', r, '--tab', '--ref', '--active',
        '-o', File.join(cli[:outdir], "#{r}.tsv")
      ]
    )
  end
  call_cli(['browse', '-P', cli[:outdir]])
end

#transfer_metadata(obj, md) ⇒ Object 



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# File 'lib/miga/cli/action/wf.rb', line 270

def transfer_metadata(obj, md)
  # Clear old metadata
  obj.metadata.each do |k, v|
    obj.metadata[k] = nil if k.to_s =~ /^run_/ || obj.option?(k)
  end
  # Transfer and save
  md.each { |k, v| obj.metadata[k] = v }
  obj.save
end