miga-base 1.2.9.0 → 1.2.10.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: '091cbb355cb05e9f9b78a84222ce575755e4f5fc134b7b86c3543a40297776ce'
-  data.tar.gz: 04b636a84a89030128b4a267a8a0c49013161fc753c7e7f5fe29b767f4095ee4
+  metadata.gz: 22d59bdb8dee84becd895fa7cd7be47912f3b895025494e55fb46b7125ac5560
+  data.tar.gz: d7213e012fa9b110d5391f5957cd3b2336e41a7ad84775471beca7da3c9510e3
 SHA512:
-  metadata.gz: b85165b51ec14d4fb3d78eb7945938b253e53d1aafee6593252dc54bd8202bc5709812cbbc22cc1d01a1b351f4843769e77aab1f92447a68a0ebe604e0adf150
-  data.tar.gz: e7edbc1aeec3119d69503fef00be330783eef5afb9e03dc24077ed87e596d1c7f8bac325e7d45caacda7924bcec442d5e0dbc6a90e5cb506ae7b77f73f06840f
+  metadata.gz: ecfd6595931a7fb0fd9b924a8a7cc64535a78ab97a1a978a65f0861e719d8570ef4ac34da8587a23664e84c215b67efdaac059d1aa159da318750dd75ebab04d
+  data.tar.gz: cda07a76118f2cba313deb974d8f6397612e11dd619332a707e12898afbb1d199bb8eeef07485c95826ddaa7b15adb617475168b668b201f59b7acc424afff84

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, 0].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, 11, 28)
 
   ##
   # 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: 1.2.10.0
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2022-10-15 00:00:00.000000000 Z
+date: 2022-11-28 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons