<commit_before># @package MiGA
# @license Artistic-2.0

class MiGA::Dataset < MiGA::MiGA

  # Class-level
  class << self
    def RESULT_DIRS ; @@RESULT_DIRS ; end
    def KNOWN_TYPES ; @@KNOWN_TYPES ; end
    def PREPROCESSING_TASKS ; @@PREPROCESSING_TASKS ; end
  end
  
end

module MiGA::Dataset::Base
  
  ##
  # Directories containing the results from dataset-specific tasks.
  @@RESULT_DIRS = {
    # 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"
  }

  ##
  # Supported dataset types.
  @@KNOWN_TYPES = {
    genome: {description: 'The genome from an isolate.', multi: false},
    scgenome: {description: 'A Single-cell Amplidied Genome (SAG).',
      multi: false},
    popgenome: {description: 'A Metagenome-Assembled Genome (MAG).',
      :multi=>false},
    metagenome: {description: 'A metagenome (excluding viromes).',
      multi: true},
    virome: {description: 'A viral metagenome.', multi: true}
  }

  ##
  # Returns an Array of tasks to be executed before project-wide tasks.<commit_msg>Typo and extra periods fix<commit_after># @package MiGA
# @license Artistic-2.0

class MiGA::Dataset < MiGA::MiGA

  # Class-level
  class << self
    def RESULT_DIRS ; @@RESULT_DIRS ; end
    def KNOWN_TYPES ; @@KNOWN_TYPES ; end
    def PREPROCESSING_TASKS ; @@PREPROCESSING_TASKS ; end
  end
  
end

module MiGA::Dataset::Base
  
  ##
  # Directories containing the results from dataset-specific tasks.
  @@RESULT_DIRS = {
    # 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"
  }

  ##
  # Supported dataset types.
  @@KNOWN_TYPES = {
    genome: {description: 'The genome from an isolate.', multi: false},
    scgenome: {description: 'A Single-cell Amplified Genome (SAG)',
      multi: false},
    popgenome: {description: 'A Metagenome-Assembled Genome (MAG)',
      :multi=>false},
    metagenome: {description: 'A metagenome (excluding viromes)',
      multi: true},
    virome: {description: 'A viral metagenome', multi: true}
  }

  ##
  # Returns an Array of tasks to be executed before project-wide tasks.
{'fraction_non_alphanumeric': 0.13123190736571244, 'fraction_numerical': 0.029591508523641043, 'mean_word_length': 3.6348733233979136, 'pattern_counts': {'":': 0, '<': 9, '<?xml version=': 0, '>': 5, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '205184', 'n_tokens_mistral': 1161, 'n_tokens_neox': 1068, 'n_words': 251}