class CagnutPicard::CollectGcBiasMetrics

Public Class Methods

new(opts = {}) click to toggle source
# 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

Public Instance Methods

collect_gc_bias_metrics_options() click to toggle source
# 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() click to toggle source
# 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() click to toggle source
# 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() click to toggle source
# 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) click to toggle source
# 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) click to toggle source
# 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