class CagnutPipelineDraw::Pipeline::Recalibration

Attributes

gatk[RW]
picard[RW]
samtools[RW]

Public Class Methods

new(job_name) click to toggle source
# File lib/cagnut_pipeline_draw/pipeline/recalibration.rb, line 6
def initialize job_name
  @job_name = job_name
  @config = Cagnut::Configuration.config
  @gatk = ::CagnutGatk::Util.new @config
  @picard = ::CagnutPicard::Util.new @config
  @samtools = ::CagnutSamtools::Util.new
end

Public Instance Methods

run(filename = nil, order=1) click to toggle source
# File lib/cagnut_pipeline_draw/pipeline/recalibration.rb, line 14
def run filename = nil, order=1
  job_name, filename, order = picard.markdup picard_markup_dirs, order, @job_name, filename
  order = samtools.do_flag_stat samtools_do_flag_stat_dirs, order, job_name, filename
  order = gatk.count_read gatk_count_read_dirs, order, job_name, filename
  job_name, filename, order = gatk.recal gatk_recal_dirs, order, job_name, filename
  order = picard.picard_qc_metrics picard_picard_qc_metrics_dirs, order, job_name, filename
  [job_name, filename, order]
end

Private Instance Methods

gatk_count_read_dirs() click to toggle source
# File lib/cagnut_pipeline_draw/pipeline/recalibration.rb, line 40
def gatk_count_read_dirs
  {
    input: @config['sample']['bam'],
    output: @config['sample']['stat']
  }
end
gatk_recal_dirs() click to toggle source
# File lib/cagnut_pipeline_draw/pipeline/recalibration.rb, line 47
def gatk_recal_dirs
  {
    input: @config['sample']['bam'],
    output: @config['sample']['bam'],
    contrast: @config['sample']['bam']
  }
end
picard_markup_dirs() click to toggle source
# File lib/cagnut_pipeline_draw/pipeline/recalibration.rb, line 25
def picard_markup_dirs
  {
    input: @config['sample']['bam'],
    output: @config['sample']['bam'],
    tmp_dir: @config['sample']['tmp']
  }
end
picard_picard_qc_metrics_dirs() click to toggle source
# File lib/cagnut_pipeline_draw/pipeline/recalibration.rb, line 55
def picard_picard_qc_metrics_dirs
  {
    input: @config['sample']['bam'],
    output: @config['sample']['stat'],
    tmp_dir: @config['sample']['tmp']
  }
end
samtools_do_flag_stat_dirs() click to toggle source
# File lib/cagnut_pipeline_draw/pipeline/recalibration.rb, line 33
def samtools_do_flag_stat_dirs
  {
    input: @config['sample']['bam'],
    output: @config['sample']['stat']
  }
end