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
- #call_cli(cmd) ⇒ Object
- #cleanup ⇒ Object
- #create_project(stage, p_metadata = {}, d_metadata = {}) ⇒ Object
- #default_opts_for_wf ⇒ Object
- #download_datasets ⇒ Object
- #import_datasets(stage) ⇒ Object
- #initialize_empty_project(metadata) ⇒ Object
- #opts_for_wf(opt, files_desc, params = {}) ⇒ Object
- #opts_for_wf_distances(opt) ⇒ Object
- #run_daemon ⇒ Object
- #summarize(which = %w[cds assembly essential_genes ssu]) ⇒ Object
- #transfer_metadata(obj, md) ⇒ Object
Instance Method Details
#call_cli(cmd) ⇒ Object
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# File 'lib/miga/cli/action/wf.rb', line 243 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 233 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.(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 142 def create_project(stage, = {}, = {}) 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() download_datasets import_datasets(stage) # Define datasets metadata p.load [:type] = cli[:dataset_type] p.each_dataset { |d| (d, ) } 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 178 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 204 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 163 def initialize_empty_project() 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') [:type] = cli[:project_type] (p, ) %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( '--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)' ) { |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 249 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 217 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 263 def (obj, md) # Clear old metadata obj..each do |k, v| obj.[k] = nil if k.to_s =~ /^run_/ || obj.option?(k) end # Transfer and save md.each { |k, v| obj.[k] = v } obj.save end |