Module: Cagnut::Cli::Pipeline::Draw

Defined in:
lib/cagnut_pipeline_draw/cli/pipeline/draw.rb

Instance Method Summary collapse

Instance Method Details

#pipeline_draw(opts = {}) ⇒ Object 



6
7
8
9
10
 
# 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 = {}, order = 1) ⇒ Object 



12
13
14
15
 
# 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 = {}, order = 1) ⇒ Object 



17
18
19
20
 
# 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 = {}, order = 1) ⇒ Object 



22
23
24
25
 
# 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) ⇒ Object 



27
28
29
30
 
# 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