class CagnutGatk::VariantFiltration
Public Class Methods
new(opts = {})
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# File lib/cagnut_gatk/functions/variant_filtration.rb, line 9 def initialize opts = {} @order = sprintf '%02i', opts[:order] @input = opts[:input].nil? ? "#{opts[:dirs][:input]}/#{sample_name}.vcf" : opts[:input] @job_name = "#{prefix_name}_snpFiltr_#{sample_name}" @output = "#{opts[:dirs][:output]}/#{sample_name}_filtered.vcf" end
Public Instance Methods
cluster_options(previous_job_id = nil)
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# File lib/cagnut_gatk/functions/variant_filtration.rb, line 23 def cluster_options previous_job_id = nil { previous_job_id: previous_job_id, adjust_memory: ['h_stack=256M', 'h_vmem=10G'], tools: ['gatk', 'variant_filtration'] } end
generate_script()
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# File lib/cagnut_gatk/functions/variant_filtration.rb, line 52 def generate_script script_name = "#{@order}_gatk_variant_filtration" 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 $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs" if [ ! -s "#{@input}.idx" ]; then echo "Incomplete VCF:" #{@input} exit 100 fi #{params_combination['java'].join("\s")} \\ #{params_combination['params'].join(" \\\n ")} \\ #{::Cagnut::JobManage.run_local} EXITSTATUS=$? #if [ ! -s "#{@output}" ]; then exit 100;fi; if [ ! -s "#{@output}.idx" ] then echo "vcf incomplete!" 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/variant_filtration.rb, line 47 def modified_java_array array = variant_filtration_params['java'].dup array.unshift(java_path).uniq end
params_combination()
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# File lib/cagnut_gatk/functions/variant_filtration.rb, line 31 def params_combination @params_combination_hash ||= { 'java' => modified_java_array, 'params' => variant_filtration_options } end
run(previous_job_id = nil)
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# File lib/cagnut_gatk/functions/variant_filtration.rb, line 16 def run previous_job_id = nil puts "Submitting #{sample_name} Jobs: variant (SNPs, INDELs) -filtration" script_name = generate_script ::Cagnut::JobManage.submit script_name, @job_name, cluster_options(previous_job_id) [@job_name, @output] end
variant_filtration_options()
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# File lib/cagnut_gatk/functions/variant_filtration.rb, line 38 def variant_filtration_options array = variant_filtration_params['params'].dup array << "-T VariantFiltration" array << "-R #{ref_fasta}" array << "--variant:VCF #{@input}" array << "-o #{@output}" array.uniq end