module Cagnut::Cli::Pipeline::Draw
Public Instance Methods
pipeline_draw(opts = {})
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# 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 = {})
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# 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 = {})
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# 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 = {})
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# 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)
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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