module Cagnut::Cli::Pipeline::Draw

Public Instance Methods

pipeline_draw(opts = {}) click to toggle source
# File lib/cagnut_pipeline_draw/cli/pipeline/draw.rb, line 6
def pipeline_draw opts = {}
  opts[:job_name], opts[:filename], order = pipeline_draw1
  opts[:job_name], opts[:filename], order = pipeline_draw2 opts, order
  opts[:job_name], opts[:filename], order = pipeline_draw3 opts, order
end
pipeline_draw1(opts = {}) click to toggle source
# File lib/cagnut_pipeline_draw/cli/pipeline/draw.rb, line 12
def pipeline_draw1 opts = {}, order=1
  puts 'Phase 1 - Create BAM alignments'
  CagnutPipelineDraw::Pipeline::Alignment.new.run order
end
pipeline_draw2(opts = {}) click to toggle source
# File lib/cagnut_pipeline_draw/cli/pipeline/draw.rb, line 17
def pipeline_draw2 opts = {}, order=1
  puts 'Phase 2 - BAM Recalibration'
  CagnutPipelineDraw::Pipeline::Recalibration.new(opts[:job_name]).run opts[:filename], order
end
pipeline_draw3(opts = {}) click to toggle source
# File lib/cagnut_pipeline_draw/cli/pipeline/draw.rb, line 22
def pipeline_draw3 opts = {}, order=1
  puts 'Phase 3 - VariantCall and Generate Stats'
  CagnutPipelineDraw::Pipeline::VariantCall.new(opts[:job_name]).run opts[:filename], order
end
run_filter(names) click to toggle source
Calls superclass method
# File lib/cagnut_pipeline_draw/cli/pipeline/draw.rb, line 27
def run_filter names
  return if names.size <= 3 && names.all? { |name| CagnutPipelineDraw.pipeline_names.include? name }
  super
end