class CagnutPicard::MeanQualityByCycle
Public Class Methods
new(opts = {})
click to toggle source
# File lib/cagnut_picard/functions/mean_quality_by_cycle.rb, line 9 def initialize opts = {} @order = sprintf '%02i', opts[:order] @tmp_dir = opts[:dirs][:tmp_dir] @job_name = "#{prefix_name}_meanQbycycle_#{sample_name}" @input = opts[:input].nil? ? "#{opts[:dirs][:input]}/#{sample_name}_recal.bam" : opts[:input] @output = "#{opts[:dirs][:output]}/quality_table" @chart_output= "#{opts[:dirs][:output]}/qualityByCycle_#{sample_name}.pdf" end
Public Instance Methods
generate_script()
click to toggle source
# File lib/cagnut_picard/functions/mean_quality_by_cycle.rb, line 55 def generate_script script_name = "#{@order}_picard_meanQbycycle" 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
mean_quality_by_cycle_options()
click to toggle source
# File lib/cagnut_picard/functions/mean_quality_by_cycle.rb, line 33 def mean_quality_by_cycle_options array = mean_quality_by_cycle_params['params'].dup array << "INPUT=#{@input}" array << "OUTPUT=#{@output}" array << "TMP_DIR=#{@tmp_dir}" array << "CHART_OUTPUT=#{@chart_output}" array.uniq end
modified_java_array()
click to toggle source
# File lib/cagnut_picard/functions/mean_quality_by_cycle.rb, line 42 def modified_java_array array = mean_quality_by_cycle_params['java'].dup array << 'MeanQualityByCycle' array.unshift(java_path).uniq end
params_combination_hash()
click to toggle source
# File lib/cagnut_picard/functions/mean_quality_by_cycle.rb, line 48 def params_combination_hash @params_combination_hash ||= { 'java' => modified_java_array, 'params' => mean_quality_by_cycle_options } end
queuing_options(previous_job_id = nil)
click to toggle source
# File lib/cagnut_picard/functions/mean_quality_by_cycle.rb, line 25 def queuing_options previous_job_id = nil { previous_job_id: previous_job_id, adjust_memory: ['h_vmem=5G'], tools: ['picard', 'mean_quality_by_cycle'] } end
run(previous_job_id = nil)
click to toggle source
# File lib/cagnut_picard/functions/mean_quality_by_cycle.rb, line 18 def run previous_job_id = nil puts "Submitting Picard MeanQualityByCycle #{sample_name} Jobs" script_name = generate_script ::Cagnut::JobManage.submit script_name, @job_name, queuing_options(previous_job_id) @job_name end