class CagnutGatk::RealignerTargetCreator
Public Class Methods
new(opts = {})
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# File lib/cagnut_gatk/functions/realigner_target_creator.rb, line 10 def initialize opts = {} @order = sprintf '%02i', opts[:order] @job_name = "#{prefix_name}_realignTargetCreator_#{sample_name}" @input = opts[:input].nil? ? "#{opts[:dirs][:input]}/#{sample_name}_markdup.bam" : opts[:input] @output = "#{opts[:dirs][:output]}/#{sample_name}_markdup.interval_list" end
Public Instance Methods
cluster_options(previous_job_id = nil)
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# File lib/cagnut_gatk/functions/realigner_target_creator.rb, line 24 def cluster_options previous_job_id = nil core_num = 6 job_mem1 = "adjustWorkingMem 256M #{core_num}" job_mem2 = "adjustWorkingMem 10G #{core_num}" { previous_job_id: previous_job_id, var_env: [core_num], adjust_memory: ["h_stack=#{job_mem1}", "h_vmem=#{job_mem2}"], parallel_env: [core_num], tools: ['gatk', 'realigner_target_creator'] } end
generate_script()
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# File lib/cagnut_gatk/functions/realigner_target_creator.rb, line 61 def generate_script script_name = "#{@order}_gatk_realigner_target_creator" 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 $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs" #{params_combination['java'].join("\s")} \\ #{params_combination['params'].join(" \\\n ")} \\ #{::Cagnut::JobManage.run_local} EXITSTATUS=$? #force error when missing output if [ ! -s "#{@output}" ] then echo "Missing indel_calls #{@output}, can not continue" 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()
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# File lib/cagnut_gatk/functions/realigner_target_creator.rb, line 49 def modified_java_array array = realigner_target_creator_params['java'].dup array.unshift(java_path).uniq end
params_combination()
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# File lib/cagnut_gatk/functions/realigner_target_creator.rb, line 54 def params_combination @params_combination_hash ||= { 'java' => modified_java_array, 'params' => realigner_target_creator_options } end
realigner_target_creator_options()
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# File lib/cagnut_gatk/functions/realigner_target_creator.rb, line 37 def realigner_target_creator_options array = realigner_target_creator_params['params'].dup array << "-T RealignerTargetCreator" array << "-R #{ref_fasta}" array << "--known #{snpdb}" array << "-I #{@input}" array << "-o #{@output}" array << "-L #{target_flanks_file}" if target_flanks_file array.uniq! array.uniq end
run(previous_job_id = nil)
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# File lib/cagnut_gatk/functions/realigner_target_creator.rb, line 17 def run previous_job_id = nil puts "Submitting realigner_target_creator #{sample_name}" script_name = generate_script ::Cagnut::JobManage.submit script_name, @job_name, cluster_options(previous_job_id) [@job_name, @output] end