class Cagnut::Configuration::Base

Attributes

cluster[RW]
data_type[RW]
dbsnp_ref_indels[RW]
dodebug[RW]
java_path[RW]
jobs_dir[RW]
magic28[RW]
pipeline_name[RW]
prefix_name[RW]
ref_fasta[RW]
sample_name[RW]
seqs_path[RW]
snpdb[RW]
target[RW]
target_flanks_file[RW]

Public Class Methods

load(config) click to toggle source
# File lib/cagnut/configuration/base.rb, line 12
def load config
  instance.load config
end

Public Instance Methods

attributes() click to toggle source
# File lib/cagnut/configuration/base.rb, line 24
def attributes
  {
    prefix_name: @config['prefix_name'],
    sample_name: @config['sample']['name'],
    dodebug: @config['dodebug'],
    java_path: @config['tools']['java'],
    ref_fasta: @config['refs']['ref_fasta'],
    snpdb: @config['refs']['dbsnp']['ref'],
    dbsnp_ref_indels: @config['refs']['dbsnp']['indels'],
    target: @config['refs']['targets_file'],
    target_flanks_file: @config['refs']['target_flanks_file'],
    magic28: '1f8b08040000000000ff0600424302001b0003000000000000000000',
    seqs_path: @config['sample']['seqs_path'],
    data_type: @config['info']['data_type'],
    jobs_dir: @config['sample']['jobs'],
    cluster: @config['cluster']
  }
end
load(config) click to toggle source
# File lib/cagnut/configuration/base.rb, line 17
def load config
  @config = config
  attributes.each do |name, value|
    send "#{name}=", value if respond_to? "#{name}="
  end
end