miga-base 1.2.9.0 → 1.2.10.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: '091cbb355cb05e9f9b78a84222ce575755e4f5fc134b7b86c3543a40297776ce'
-  data.tar.gz: 04b636a84a89030128b4a267a8a0c49013161fc753c7e7f5fe29b767f4095ee4
+  metadata.gz: 43040e5cfb781472a3b329f927def556241354dbe5b2bce0cf1193343a54f9e3
+  data.tar.gz: 4c189d36e1fe8bc0e1c9ba43d727e8db8c6cda4607b6c43b348ea6f662d50a28
 SHA512:
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-  data.tar.gz: e7edbc1aeec3119d69503fef00be330783eef5afb9e03dc24077ed87e596d1c7f8bac325e7d45caacda7924bcec442d5e0dbc6a90e5cb506ae7b77f73f06840f
+  metadata.gz: c0dd101a62434880a0458eeb00fb4a1acdfe21eeda37b2f3c240cb0b5713b0631a79a994a4bcc7c030403f0bb82d4c1107fbca0c92e6f7d33247d55896b9eabf
+  data.tar.gz: b5d09fbab61dfff05393e2408e56b61d3208d8c8f3293125cc25f880a03baaa23fbd44a7612a8453d959c42fe8d41a826e35d10c597de3ac6baebbc9198ff498

data/lib/miga/cli/action/classify_wf.rb

@@ -60,13 +60,16 @@ class MiGA::Cli::Action::ClassifyWf < MiGA::Cli::Action
     )
     p.set_option(:ref_project, ref_db.path)
     p.set_option(:tax_pvalue, cli[:pvalue])
+
     # Run
     run_daemon
     summarize(%w[cds assembly essential_genes]) if cli[:summaries]
-    summarize(['taxonomy'])
-    cli.say "Summary: classification"
-    ofile = File.expand_path('classification.tsv', cli[:outdir])
-    call_cli(['ls', '-P', cli[:outdir], '-m', 'tax', '--tab', '-o', ofile])
+    summarize(%w[taxonomy])
+    unless cli[:prepare_and_exit]
+      cli.say "Summary: classification"
+      ofile = File.expand_path('classification.tsv', cli[:outdir])
+      call_cli(['ls', '-P', cli[:outdir], '-m', 'tax', '--tab', '-o', ofile])
+    end
     cleanup
   end
 

data/lib/miga/cli/action/derep_wf.rb

@@ -68,6 +68,8 @@ class MiGA::Cli::Action::DerepWf < MiGA::Cli::Action
   private
 
   def dereplicate(p)
+    return if cli[:prepare_and_exit]
+
     cli.say 'Extracting genomospecies clades'
     r = p.result(:clade_finding) or raise 'Result unavailable: run failed'
     c_f = r.file_path(:clades_gsp) or raise 'Result incomplete: run failed'

data/lib/miga/cli/action/index_wf.rb

@@ -26,6 +26,7 @@ class MiGA::Cli::Action::IndexWf < MiGA::Cli::Action
   def perform
     # Input data
     p = create_project(:assembly, {}, run_mytaxa_scan: cli[:mytaxa])
+
     # Run
     run_daemon
     summarize

data/lib/miga/cli/action/preproc_wf.rb

@@ -41,6 +41,7 @@ class MiGA::Cli::Action::PreprocWf < MiGA::Cli::Action
       d_metadata[:run_mytaxa] = false
     end
     p = create_project(cli[:input_type], p_metadata, d_metadata)
+
     # Run
     run_daemon
     summarize

data/lib/miga/cli/action/quality_wf.rb

@@ -28,10 +28,11 @@ class MiGA::Cli::Action::QualityWf < MiGA::Cli::Action
     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]
+    if cli[:mytaxa] && !cli[:prepare_and_exit]
       dir = File.expand_path('mytaxa_scan', cli[:outdir])
       Dir.mkdir(dir)
       p.each_dataset do |d|

data/lib/miga/cli/action/wf.rb

@@ -8,7 +8,8 @@ module MiGA::Cli::Action::Wf
     cli.expect_files = true
     cli.defaults = {
       clean: false, project_type: :genomes, dataset_type: :popgenome,
-      ncbi_draft: true, min_qual: MiGA::Project.OPTIONS[:min_qual][:default]
+      ncbi_draft: true, min_qual: MiGA::Project.OPTIONS[:min_qual][:default],
+      prepare_and_exit: false
     }
   end
 
@@ -83,6 +84,10 @@ module MiGA::Cli::Action::Wf
       '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
 
   def opts_for_wf_distances(opt)
@@ -159,6 +164,8 @@ module MiGA::Cli::Action::Wf
   end
 
   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(
@@ -173,6 +180,7 @@ module MiGA::Cli::Action::Wf
   end
 
   def cleanup
+    return if cli[:prepare_and_exit]
     return unless cli[:clean]
 
     cli.say 'Cleaning up intermediate files'
@@ -188,6 +196,8 @@ module MiGA::Cli::Action::Wf
   end
 
   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]

data/lib/miga/version.rb

@@ -12,7 +12,7 @@ module MiGA
   # - String indicating release status:
   #   - rc* release candidate, not released as gem
   #   - [0-9]+ stable release, released as gem
-  VERSION = [1.2, 9, 0].freeze
+  VERSION = [1.2, 10, 1].freeze
 
   ##
   # Nickname for the current major.minor version.
@@ -20,7 +20,7 @@ module MiGA
 
   ##
   # Date of the current gem relese.
-  VERSION_DATE = Date.new(2022, 10, 15)
+  VERSION_DATE = Date.new(2022, 12, 1)
 
   ##
   # References of MiGA

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.2.9.0
+  version: 1.2.10.1
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2022-10-15 00:00:00.000000000 Z
+date: 2022-12-01 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons