Class: CagnutPicard::CollectGcBiasMetrics

Inherits:
Object
  • Object
show all
Extended by:
Forwardable
Defined in:
lib/cagnut_picard/functions/collect_gc_bias_metrics.rb

Instance Method Summary collapse

Constructor Details

#initialize(opts = {}) ⇒ CollectGcBiasMetrics

Returns a new instance of CollectGcBiasMetrics.



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# File 'lib/cagnut_picard/functions/collect_gc_bias_metrics.rb', line 9

def initialize opts = {}
  @order = sprintf '%02i', opts[:order]
  @tmp_dir = opts[:dirs][:tmp_dir]
  @job_name = "#{prefix_name}_collect_gc_bias_metrics_#{sample_name}"
  @input = opts[:input].nil? ? "#{opts[:dirs][:input]}/#{sample_name}_recal.bam" : opts[:input]
  @output = "#{opts[:dirs][:output]}/Gc_Bias_Metrics"
  @chart_output = "#{opts[:dirs][:output]}/Gc_bias_#{sample_name}.pdf"
  @summary_output = "#{opts[:dirs][:output]}/sum_out_gc"
end

Instance Method Details

#collect_gc_bias_metrics_options ⇒ Object 



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# File 'lib/cagnut_picard/functions/collect_gc_bias_metrics.rb', line 34

def collect_gc_bias_metrics_options
  array = collect_gc_bias_metrics_params['params'].dup
  array << "REFERENCE_SEQUENCE=#{ref_fasta}"
  array << "TMP_DIR=#{@tmp_dir}"
  array << "INPUT=#{@input}"
  array << "OUTPUT=#{@output}"
  array << "CHART_OUTPUT=#{@chart_output}"
  array << "SUMMARY_OUTPUT=#{@summary_output}"
  array.uniq
end

#generate_script ⇒ Object 



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# File 'lib/cagnut_picard/functions/collect_gc_bias_metrics.rb', line 58

def generate_script
  script_name = "#{@order}_picard_collect_gc_bias_metrics"
  file = File.join jobs_dir, "#{script_name}.sh"
  File.open(file, 'w') do |f|
    f.puts <<-BASH.strip_heredoc
      #!/bin/bash

      cd "#{jobs_dir}/../"
      echo "#{script_name} is starting at $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"
      #{params_combination_hash['java'].join("\s")} \\
        #{params_combination_hash['params'].join(" \\\n            ")} \\
        #{::Cagnut::JobManage.run_local}

      EXITSTATUS=$?
      if [ ! -s "#{@chart_output}" ]; then exit 100;fi;
      echo "#{script_name} is finished at $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"

      exit $EXITSTATUS
    BASH
  end
  File.chmod(0700, file)
  script_name
end

#modified_java_array ⇒ Object 



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# File 'lib/cagnut_picard/functions/collect_gc_bias_metrics.rb', line 45

def modified_java_array
  array = collect_gc_bias_metrics_params['java'].dup
  array << 'CollectGcBiasMetrics'
  array.unshift(java_path).uniq
end

#params_combination_hash ⇒ Object 



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# File 'lib/cagnut_picard/functions/collect_gc_bias_metrics.rb', line 51

def params_combination_hash
  @params_combination_hash ||= {
    'java' => modified_java_array,
    'params' => collect_gc_bias_metrics_options
  }
end

#queuing_options(previous_job_id = nil) ⇒ Object 



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# File 'lib/cagnut_picard/functions/collect_gc_bias_metrics.rb', line 26

def queuing_options previous_job_id = nil
  {
    previous_job_id: previous_job_id,
    adjust_memory: ['h_vmem=5G'],
    tools: ['picard', 'collect_gc_bias_metrics']
  }
end

#run(previous_job_id = nil) ⇒ Object 



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# File 'lib/cagnut_picard/functions/collect_gc_bias_metrics.rb', line 19

def run previous_job_id = nil
  puts "Submitting Picard CollectGcBiasMetrics #{sample_name} Jobs "
  script_name = generate_script
  ::Cagnut::JobManage.submit script_name, @job_name, queuing_options(previous_job_id)
  @job_name
end