class CagnutGatk::VariantEval
Public Class Methods
new(opts = {})
click to toggle source
# File lib/cagnut_gatk/functions/variant_eval.rb, line 9 def initialize opts = {} @order = sprintf '%02i', opts[:order] @vcf_dir = opts[:dirs][:output] @input = opts[:input].nil? ? "#{opts[:dirs][:input]}/#{sample_name}_filtered.vcf" : opts[:input] @output = "#{@vcf_dir}/#{sample_name}.eval" @job_name = "#{prefix_name}_snpEval_#{sample_name}" end
Public Instance Methods
cluster_options(previous_job_id = nil)
click to toggle source
# File lib/cagnut_gatk/functions/variant_eval.rb, line 25 def cluster_options previous_job_id = nil { previous_job_id: previous_job_id, adjust_memory: ['h_stack=256M', 'h_vmem=8G'], tools: ['gatk', 'variant_eval'] } end
generate_script()
click to toggle source
# File lib/cagnut_gatk/functions/variant_eval.rb, line 56 def generate_script script_name = "#{@order}_gatk_variant_eval" file = File.join jobs_dir, "#{script_name}.sh" ltag = target.nil? ? '' : "-L #{target}" File.open(file, 'w') do |f| f.puts <<-BASH.strip_heredoc #!/bin/bash cd "#{jobs_dir}/../" echo "#{script_name} is starting at $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs" EVALNAME=$(basename #{@vcf_dir}/#{sample_name}) #{params_combination['java'].join("\s")} \\ #{params_combination['params'].join(" \\\n ")} \\ #{::Cagnut::JobManage.run_local} EXITSTATUS=$? if [ ! -s "#{@output}" ] then echo "Missing #{@output}" exit 100 fi echo "#{script_name} is finished at $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs" exit $EXITSTATUS BASH end File.chmod(0700, file) script_name end
modified_java_array()
click to toggle source
# File lib/cagnut_gatk/functions/variant_eval.rb, line 44 def modified_java_array array = variant_eval_params['java'].dup array.unshift(java_path).uniq end
params_combination()
click to toggle source
# File lib/cagnut_gatk/functions/variant_eval.rb, line 49 def params_combination @params_combination_hash ||= { 'java' => modified_java_array, 'params' => variant_eval_options } end
run(previous_job_id = nil)
click to toggle source
# File lib/cagnut_gatk/functions/variant_eval.rb, line 17 def run previous_job_id = nil return unless snpdb puts "Submitting #{sample_name} Jobs: variant (SNPs, INDELs) -evaluation " script_name = generate_script ::Cagnut::JobManage.submit script_name, @job_name, cluster_options(previous_job_id) @job_name end
variant_eval_options()
click to toggle source
# File lib/cagnut_gatk/functions/variant_eval.rb, line 33 def variant_eval_options array = variant_eval_params['params'].dup array << "-T VariantEval" array << "-R #{ref_fasta}" array << "--dbsnp #{snpdb}" array << "-o #{@output}" array << "--eval:$EVALNAME #{@input}" array << "-L #{target}" if target array.uniq end