class CagnutPipelineDraw::Pipeline::VariantCall

Attributes

gatk[RW]
snp_eff[RW]

Public Class Methods

new(job_name) click to toggle source
# File lib/cagnut_pipeline_draw/pipeline/variant_call.rb, line 6
def initialize job_name
  @job_name = job_name
  @config = Cagnut::Configuration.config
  @gatk = ::CagnutGatk::Util.new @config
  @snpeff = ::CagnutSnpeff::Util.new
end

Public Instance Methods

run(filename = nil, order=1) click to toggle source
# File lib/cagnut_pipeline_draw/pipeline/variant_call.rb, line 13
def run filename = nil, order=1
  order = @gatk.depth_of_coverage gatk_depth_of_coverage_dirs, order, @job_name, filename
  job_name, filename, order = @gatk.unified_genotyper gatk_unified_genotyper_dirs, order, @job_name, filename
  job_name, filename, order = @gatk.snpcal gatk_snpcal_dirs, order, job_name, filename
  job_name, order = @snpeff.snp_annotation snpeff_snp_annotation_dirs, order, job_name, filename
  # collectSPeekMetrics
  [job_name, nil, order+1]
end

Private Instance Methods

gatk_depth_of_coverage_dirs() click to toggle source
# File lib/cagnut_pipeline_draw/pipeline/variant_call.rb, line 24
def gatk_depth_of_coverage_dirs
  {
    input: @config['sample']['bam'],
    output: @config['sample']['stat'],
  }
end
gatk_snpcal_dirs() click to toggle source
# File lib/cagnut_pipeline_draw/pipeline/variant_call.rb, line 31
def gatk_snpcal_dirs
  {
    input: @config['sample']['bam'],
    output: @config['sample']['vcf'],
  }
end
gatk_unified_genotyper_dirs() click to toggle source
# File lib/cagnut_pipeline_draw/pipeline/variant_call.rb, line 38
def gatk_unified_genotyper_dirs
  {
    input: @config['sample']['vcf'],
    output: @config['sample']['vcf'],
  }
end
snpeff_snp_annotation_dirs() click to toggle source
# File lib/cagnut_pipeline_draw/pipeline/variant_call.rb, line 45
def snpeff_snp_annotation_dirs
  {
    input: @config['sample']['vcf'],
    output: @config['sample']['vcf'],
  }
end