Module: MiGA::Project::Base

Included in:
Result
Defined in:
lib/miga/project/base.rb

Constant Summary collapse

@@FOLDERS =

Top-level folders inside a project

%w[data metadata daemon]
@@DATA_FOLDERS =

Folders for results

%w[
  01.raw_reads 02.trimmed_reads 03.read_quality 04.trimmed_fasta
  05.assembly 06.cds
  07.annotation 07.annotation/01.function 07.annotation/02.taxonomy
  07.annotation/01.function/01.essential
  07.annotation/01.function/02.ssu
  07.annotation/02.taxonomy/01.mytaxa
  07.annotation/03.qa 07.annotation/03.qa/01.checkm
  07.annotation/03.qa/02.mytaxa_scan
  08.mapping 08.mapping/01.read-ctg 08.mapping/02.read-gene
  09.distances 09.distances/01.haai 09.distances/02.aai
  09.distances/03.ani 09.distances/04.ssu 09.distances/05.taxonomy
  10.clades 10.clades/01.find 10.clades/02.ani 10.clades/03.ogs
  10.clades/04.phylogeny 10.clades/04.phylogeny/01.essential
  10.clades/04.phylogeny/02.core 10.clades/05.metadata
  90.stats
]
@@RESULT_DIRS =

Directories containing the results from project-wide tasks

{
  project_stats: '90.stats',
  # Distances
  haai_distances: '09.distances/01.haai',
  aai_distances: '09.distances/02.aai',
  ani_distances: '09.distances/03.ani',
  # ssu_distances: '09.distances/04.ssu',
  # Clade identification
  clade_finding: '10.clades/01.find',
  # Clade analysis
  subclades: '10.clades/02.ani',
  ogs: '10.clades/03.ogs'
  # ess_phylogeny: '10.clades/04.phylogeny/01.essential',
  # core_phylogeny: '10.clades/04.phylogeny/02.core',
  # clade_metadata: '10.clades/05.metadata'
}
@@KNOWN_TYPES =

Supported types of projects

{
  mixed: {
    description: 'Mixed collection of genomes, metagenomes, and viromes',
    single: true, multi: true
  },
  genomes: {
    description: 'Collection of genomes',
    single: true, multi: false
  },
  clade: {
    description: 'Collection of closely-related genomes (ANI >= 90%)',
    single: true, multi: false
  },
  metagenomes: {
    description: 'Collection of metagenomes and/or viromes',
    single: false, multi: true
  }
}
@@DISTANCE_TASKS =

Project-wide distance estimations

[
  :project_stats, :haai_distances, :aai_distances, :ani_distances,
  :clade_finding
]
@@INCLADE_TASKS =

Project-wide tasks for :clade projects

[:subclades, :ogs]