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 =
Hash[@@EXCLUDE_NOREF_TASKS.map{ |i| [i,true] }]
@@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 =
Hash[@@ONLY_NONMULTI_TASKS.map{ |i| [i,true] }]
@@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 =
Hash[@@ONLY_MULTI_TASKS.map{ |i| [i,true] }]