bench.rb

require 'rbbt-util'
require 'rbbt/workflow'
require 'rbbt/workflow/remote_workflow'

module HTSBenchmark

  Rbbt.claim Rbbt.share.data.studies.GIAB do |directory|
    `wget <url1.bam> -O #{directory}/data/sample1.bam`
    `wget <url2.bam> -O #{directory}/data/sample2.bam`
    `wget <url3.bam> -O #{directory}/data/sample3.bam`
    `wget <url4.vcf> -O #{directory}/data/truch.vcf`

    Path.setup(directory)
    Open.mkdir directory.WES.orig["Sample 1"]
    Open.mkdir directory.WES.orig["Sample 2"]
    Open.mkdir directory.WES.orig["Sample 3"]

    Open.ln_s directory.data["sample1.bam"], directory.WES.orig["Sample 1"]["sample1.bam"]
    Open.ln_s directory.data["sample2.bam"], directory.WES.orig["Sample 2"]["sample2.bam"]
    Open.ln_s directory.data["sample3.bam"], directory.WES.orig["Sample 3"]["sample3.bam"]

  end

  dep Sample, :BAM do |jobname,options|
    Rbbt.share.data.studies.GIAB.produce

    ["Sample 1", "Sample 2", "Sample 3"].collect do |s|
      {:jobname => s}
    end
  end
  dep HTS, :haplotype do |jobname,options,dependencies|

    options[:BAM_files] = dependencies
    {:inputs => options}
  end
  task :test_GIAB => :yaml do
    CMD.cmd("hap.py #{step(:haplotype).path} #{Rbbt.share.data.studies.GIAB.data["truth.vcf"].find} --output #{self.tmp_path}")
    nil
  end
end