Class: NugenTemplate

Inherits:
Object
  • Object
show all
Defined in:
lib/nugen_barcode_splitter/nugen_template.rb

Instance Method Summary collapse

Constructor Details

#initialize(fastq_multx, options) ⇒ NugenTemplate

Returns a new instance of NugenTemplate.



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# File 'lib/nugen_barcode_splitter/nugen_template.rb', line 5

def initialize(fastq_multx, options)
  @template ="gunzip -c <%= @read %> | \#{fastq_multx} \\\\\n--bcfile <%= @barcodes %> \#{options} <%= @options %> \\\\\n--prefix <%= @lane_dir %>/<%= @direction %> \\\\\n--suffix \".fq\"\n"
#    @template =<<EOF
##{fastq_multx} #{options}  <%= @barcodes %> \\
#  <(gunzip -c <%= @read %>) \\
#  -o <%= @lane_dir %>/<%= @direction %>.%.fq  \\
#  >> <%= @lane_dir %>/nugen_demultiplexing_fastq_multx.log
#EOF
end

Instance Method Details

#fill(lane, number, lane_dir, barcodes, read, is_fwd) ⇒ Object 



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# File 'lib/nugen_barcode_splitter/nugen_template.rb', line 20

def fill(lane, number, lane_dir, barcodes, read, is_fwd)
  if is_fwd
    direction = "R1_#{number}."
    options = "--bol"
  else
    direction = "R2_#{number}."
    options = "--eol"
  end
  context = {
    :lane => lane,
    :number => number,
    :lane_dir => lane_dir,
    :barcodes => barcodes,
    :read => read,
    :direction => direction,
    :options => options
  }

  eruby = Erubis::Eruby.new(@template)
  eruby.evaluate(context)
end

#to_s ⇒ Object 



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# File 'lib/nugen_barcode_splitter/nugen_template.rb', line 42

def to_s
  template = "#{@template.chomp()}"
end