Module: MiGA::Dataset::Base
- Included in:
- Result
- Defined in:
- lib/miga/dataset/base.rb
Constant Summary collapse
- @@RESULT_DIRS =
Directories containing the results from dataset-specific tasks.
{ # Preprocessing raw_reads: "01.raw_reads", trimmed_reads: "02.trimmed_reads", read_quality: "03.read_quality", trimmed_fasta: "04.trimmed_fasta", assembly: "05.assembly", cds: "06.cds", # Annotation essential_genes: "07.annotation/01.function/01.essential", ssu: "07.annotation/01.function/02.ssu", mytaxa: "07.annotation/02.taxonomy/01.mytaxa", mytaxa_scan: "07.annotation/03.qa/02.mytaxa_scan", # Distances (for single-species datasets) distances: "09.distances", taxonomy: "09.distances/05.taxonomy", # General statistics stats: "90.stats" }
- @@KNOWN_TYPES =
Supported dataset types.
{ genome: {description: "The genome from an isolate.", multi: false}, scgenome: {description: "A Single-cell Genome Amplification (SGA).", multi: false}, popgenome: {description: "A population genome (including " + "metagenomic bins).", :multi=>false}, metagenome: {description: "A metagenome (excluding viromes).", multi: true}, virome: {description: "A viral metagenome.", multi: true} }
- @@PREPROCESSING_TASKS =
Returns an Array of tasks to be executed before project-wide tasks.
[:raw_reads, :trimmed_reads, :read_quality, :trimmed_fasta, :assembly, :cds, :essential_genes, :ssu, :mytaxa, :mytaxa_scan, :distances, :taxonomy, :stats]
- @@EXCLUDE_NOREF_TASKS =
Tasks to be excluded from query datasets.
[:mytaxa_scan, :taxonomy]
- @@_EXCLUDE_NOREF_TASKS_H =
- @@ONLY_NONMULTI_TASKS =
Tasks to be executed only in datasets that are not multi-organism. These tasks are ignored for multi-organism datasets or for unknown types.
[:mytaxa_scan, :distances, :taxonomy]
- @@_ONLY_NONMULTI_TASKS_H =
- @@ONLY_MULTI_TASKS =
Tasks to be executed only in datasets that are multi-organism. These tasks are ignored for single-organism datasets or for unknwon types.
[:mytaxa]
- @@_ONLY_MULTI_TASKS_H =