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]