class CagnutSamtools::DoFlagStat
Public Class Methods
new(opts = {})
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# File lib/cagnut_samtools/functions/do_flag_stat.rb, line 9 def initialize opts = {} @order = sprintf '%02i', opts[:order] @job_name = "#{prefix_name}_doFlagStat_#{sample_name}" @input = opts[:input].nil? ? "#{opts[:dirs][:input]}/#{sample_name}_markdup.bam" : opts[:input] @output = "#{opts[:dirs][:output]}/#{sample_name}_merged_markdup.flagstat" end
Public Instance Methods
generate_script()
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# File lib/cagnut_samtools/functions/do_flag_stat.rb, line 31 def generate_script script_name = "#{@order}_samtools_do_flag_stat" file = File.join jobs_dir, "#{script_name}.sh" File.open(file, 'w') do |f| f.puts <<-BASH.strip_heredoc #!/bin/bash echo "#{script_name} is starting at $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs" #{samtools_path} flagstat #{@input} > #{@output} \\ #{::Cagnut::JobManage.run_local} if [ ! -s #{@output} ] then echo "Incomplete output file #{@output}" exit 100 fi echo "#{script_name} is finished at $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs" BASH end File.chmod(0700, file) script_name end
queuing_options(previous_job_id = nil)
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# File lib/cagnut_samtools/functions/do_flag_stat.rb, line 23 def queuing_options previous_job_id = nil { previous_job_id: previous_job_id, adjust_memory: ['h_vmem=500M'], tools: ['samtools', 'do_flag_stat'] } end
run(previous_job_id = nil)
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# File lib/cagnut_samtools/functions/do_flag_stat.rb, line 16 def run previous_job_id = nil puts "Submitting doFlagStat for #{sample_name}_markdup suffix" script_name = generate_script ::Cagnut::JobManage.submit script_name, @job_name, queuing_options(previous_job_id) @job_name end