class CagnutGatk::VariantFiltration

Public Class Methods

new(opts = {}) click to toggle source
# 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) click to toggle source
# 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() click to toggle source
# 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() click to toggle source
# 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() click to toggle source
# 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) click to toggle source
# 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() click to toggle source
# 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