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]