class CagnutPicard::Markdup
Public Class Methods
new(opts = {})
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# File lib/cagnut_picard/functions/markdup.rb, line 9 def initialize opts = {} @order = sprintf '%02i', opts[:order] @tmp_dir = opts[:dirs][:tmp_dir] @job_name = "#{prefix_name}_markdup_#{sample_name}" @input = opts[:input].nil? ? "#{opts[:dirs][:input]}/#{sample_name}_merged.bam" : opts[:input] @output = "#{opts[:dirs][:output]}/#{sample_name}_markdup.bam" end
Public Instance Methods
generate_script()
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# File lib/cagnut_picard/functions/markdup.rb, line 53 def generate_script script_name = "#{@order}_picard_markdup" 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 [ ! -e "#{@output}" ] then echo "Missing output: #{@output}" exit 100 fi # Check BAM EOF BAM_28=$(tail -c 28 #{@output}|xxd -p) if [ "#{magic28}" != "$BAM_28" ] then echo "Error with BAM EOF" 1>&2 exit 100 fi if [ $EXITSTATUS -ne 0 ];then exit $EXITSTATUS;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
markduplicate_options()
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# File lib/cagnut_picard/functions/markdup.rb, line 32 def markduplicate_options array = markduplicate_params['params'].dup array << "INPUT=#{@input}" array << "OUTPUT=#{@output}" array << "TMP_DIR=#{@tmp_dir}" array.uniq end
modified_java_array()
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# File lib/cagnut_picard/functions/markdup.rb, line 40 def modified_java_array array = markduplicate_params['java'].dup array << 'MarkDuplicates' array.unshift(java_path).uniq end
params_combination_hash()
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# File lib/cagnut_picard/functions/markdup.rb, line 46 def params_combination_hash @params_combination_hash ||= { 'java' => modified_java_array, 'params' => markduplicate_options } end
queuing_options(previous_job_id = nil)
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# File lib/cagnut_picard/functions/markdup.rb, line 24 def queuing_options previous_job_id = nil { previous_job_id: previous_job_id, adjust_memory: ['h_vmem=5G'], tools: ['picard', 'markduplicate'] } end
run(previous_job_id = nil)
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# File lib/cagnut_picard/functions/markdup.rb, line 17 def run previous_job_id = nil puts "Submitting markdup #{sample_name}" script_name = generate_script ::Cagnut::JobManage.submit script_name, @job_name, queuing_options(previous_job_id) [@job_name, @output] end