cagnut_pipeline_draw 0.3.1

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data/.gitignore ADDED
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+ /.bundle/
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+ /.yardoc
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+ /Gemfile.lock
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+ /_yardoc/
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+ /coverage/
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+ /doc/
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+ /pkg/
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+ /spec/reports/
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+ /tmp/
data/.rspec ADDED
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+ --format documentation
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+ --color
data/.ruby-version ADDED
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+ ruby-2.3.1
data/.travis.yml ADDED
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+ sudo: false
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+ language: ruby
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+ rvm:
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+ - 2.3.1
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+ before_install: gem install bundler -v 1.12.5
data/Gemfile ADDED
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+ source 'https://rubygems.org'
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+
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+ # Specify your gem's dependencies in cagnut_pipeline_draw.gemspec
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+ gemspec
data/LICENSE.txt ADDED
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+ The MIT License (MIT)
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+
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+ Copyright (c) 2016 Goldenio Technology
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+
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+ Permission is hereby granted, free of charge, to any person obtaining a copy
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+ of this software and associated documentation files (the "Software"), to deal
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+ in the Software without restriction, including without limitation the rights
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+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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+ copies of the Software, and to permit persons to whom the Software is
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+ furnished to do so, subject to the following conditions:
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+
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+ The above copyright notice and this permission notice shall be included in
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+ all copies or substantial portions of the Software.
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+
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+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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+ THE SOFTWARE.
data/README.md ADDED
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+ # CagnutPipelineDraw
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+
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+ ## Installation
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+
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+ Add this line to your application's Gemfile:
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+
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+ ```ruby
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+ gem 'cagnut_pipeline_draw'
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+ ```
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+
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+ And then execute:
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+
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+ $ bundle
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+
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+ Or install it yourself as:
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+
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+ $ gem install cagnut_pipeline_draw
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+
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+ ## Usage
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+
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+ ## Development
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+
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+ After checking out the repo, run `bin/setup` to install dependencies. Then, run `rake spec` to run the tests. You can also run `bin/console` for an interactive prompt that will allow you to experiment.
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+
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+ To install this gem onto your local machine, run `bundle exec rake install`. To release a new version, update the version number in `version.rb`, and then run `bundle exec rake release`, which will create a git tag for the version, push git commits and tags, and push the `.gem` file to [rubygems.org](https://rubygems.org).
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+
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+ ## Contributing
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+
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+ Bug reports and pull requests are welcome on GitHub at https://github.com/[USERNAME]/cagnut_pipeline_draw.
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+
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+
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+ ## License
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+
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+ The gem is available as open source under the terms of the [MIT License](http://opensource.org/licenses/MIT).
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+
data/Rakefile ADDED
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+ require "bundler/gem_tasks"
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+ require "rspec/core/rake_task"
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+
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+ RSpec::Core::RakeTask.new(:spec)
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+
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+ task :default => :spec
data/bin/console ADDED
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+ #!/usr/bin/env ruby
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+
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+ require "bundler/setup"
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+ require "cagnut_pipeline_draw"
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+
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+ # You can add fixtures and/or initialization code here to make experimenting
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+ # with your gem easier. You can also use a different console, if you like.
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+
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+ # (If you use this, don't forget to add pry to your Gemfile!)
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+ # require "pry"
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+ # Pry.start
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+
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+ require "irb"
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+ IRB.start
data/bin/setup ADDED
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+ #!/usr/bin/env bash
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+ set -euo pipefail
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+ IFS=$'\n\t'
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+ set -vx
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+
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+ bundle install
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+
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+ # Do any other automated setup that you need to do here
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+ # coding: utf-8
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+ lib = File.expand_path('../lib', __FILE__)
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+ $LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
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+ require 'cagnut_pipeline_draw/version'
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+
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+ Gem::Specification.new do |spec|
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+ spec.name = "cagnut_pipeline_draw"
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+ spec.version = CagnutPipelineDraw::VERSION
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+ spec.authors = ['Shi-Gang Wang', 'Tse-Ching Ho']
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+ spec.email = ['seanwang@goldenio.com', 'tsechingho@goldenio.com']
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+
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+ spec.summary = %q{Cagnut Draw Pipeline}
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+ spec.description = %q{Cagnut Draw Pipeline}
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+ spec.homepage = "https://github.com/CAGNUT/cagnut_pipeline_draw"
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+ spec.license = "MIT"
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+
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+ spec.files = `git ls-files -z`.split("\x0").reject { |f| f.match(%r{^(test|spec|features)/}) }
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+ spec.bindir = "exe"
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+ spec.executables = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
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+ spec.require_paths = ["lib"]
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+
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+ spec.add_dependency 'cagnut_core'
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+ spec.add_dependency 'cagnut_bwa'
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+ spec.add_dependency 'cagnut_gatk'
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+ spec.add_dependency 'cagnut_samtools'
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+ spec.add_dependency 'cagnut_picard'
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+ spec.add_dependency 'cagnut_snpeff'
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+ spec.add_dependency 'cagnut_toolbox'
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+
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+ spec.add_development_dependency "bundler", "~> 1.12"
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+ spec.add_development_dependency "rake", "~> 10.0"
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+ spec.add_development_dependency "rspec", "~> 3.0"
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+ end
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+ require "cagnut_pipeline_draw/version"
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+ require 'cagnut_bwa'
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+ require 'cagnut_gatk'
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+ require 'cagnut_picard'
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+ require 'cagnut_samtools'
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+ require 'cagnut_snpeff'
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+ require 'cagnut_toolbox'
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+
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+ module CagnutPipelineDraw
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+ class << self
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+ def pipeline_names
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+ %W(draw1 draw2 draw3 draw)
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+ end
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+
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+ def config_name
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+ 'draw'
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+ end
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+
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+ def root
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+ ::Pathname.new File.expand_path '../..', __FILE__
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+ end
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+ end
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+ end
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+
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+ require 'cagnut_pipeline_draw/configuration'
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+ require 'cagnut_pipeline_draw/cli/new_project/draw'
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+ require 'cagnut_pipeline_draw/cli/pipeline/draw'
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+ require "cagnut_pipeline_draw/pipeline/alignment"
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+ require "cagnut_pipeline_draw/pipeline/recalibration"
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+ require "cagnut_pipeline_draw/pipeline/variant_call"
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+ module Cagnut
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+ module Cli
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+ module NewProject
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+ module Draw
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+
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+ def actgun_pipeline_draw_root
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+ CagnutPipelineDraw.root.join('templates')
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+ end
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+
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+ def copy_draw_tools_config folder
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+ draw_tools_yml = File.join(actgun_pipeline_draw_root, 'draw_tools.yml')
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+ copy_file "#{draw_tools_yml}", "#{folder}/draw_tools.yml"
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+ end
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+
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+ def draw_pipeline_dependency_gems
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+ %W(
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+ 'cagnut_core'
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+ 'cagnut_bwa'
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+ 'cagnut_gatk'
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+ 'cagnut_samtools'
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+ 'cagnut_picard'
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+ 'cagnut_snpeff'
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+ 'cagnut_toolbox'
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+ )
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+ end
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+
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+ end
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+ end
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+ end
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+ end
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+
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+ Cagnut::NewProject.prepend Cagnut::Cli::NewProject::Draw
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+ module Cagnut
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+ module Cli
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+ module Pipeline
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+ module Draw
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+
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+ def pipeline_draw opts = {}
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+ opts[:job_name], opts[:filename], order = pipeline_draw1
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+ opts[:job_name], opts[:filename], order = pipeline_draw2 opts, order
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+ opts[:job_name], opts[:filename], order = pipeline_draw3 opts, order
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+ end
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+
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+ def pipeline_draw1 opts = {}, order=1
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+ puts 'Phase 1 - Create BAM alignments'
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+ CagnutPipelineDraw::Pipeline::Alignment.new.run order
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+ end
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+
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+ def pipeline_draw2 opts = {}, order=1
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+ puts 'Phase 2 - BAM Recalibration'
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+ CagnutPipelineDraw::Pipeline::Recalibration.new(opts[:job_name]).run opts[:filename], order
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+ end
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+
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+ def pipeline_draw3 opts = {}, order=1
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+ puts 'Phase 3 - VariantCall and Generate Stats'
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+ CagnutPipelineDraw::Pipeline::VariantCall.new(opts[:job_name]).run opts[:filename], order
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+ end
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+
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+ def run_filter names
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+ return if names.size <= 3 && names.all? { |name| CagnutPipelineDraw.pipeline_names.include? name }
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+ super
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+ end
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+
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+ end
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+ end
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+ end
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+ end
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+
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+ Cagnut::Pipeline::Base.prepend Cagnut::Cli::Pipeline::Draw
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+ Cagnut::Pipeline::Base.register CagnutPipelineDraw
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+ module CagnutPipelineDraw
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+ module Configuration
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+
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+ module Utils
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+ class << self
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+ def create_output_dirs config, index, dir
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+ draw_pipeline_folders.each do |folder_name|
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+ FileUtils.mkdir_p "#{dir}/#{folder_name}"
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+ config['samples'][index]["#{folder_name}"] = "#{dir}/#{folder_name}"
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+ end
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+ end
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+
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+ def draw_pipeline_folders
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+ %W(
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+ bam
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+ csv
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+ fastq
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+ qseq
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+ stat
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+ sai
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+ sam
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+ tmp
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+ vcf
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+ )
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+ end
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+ end
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+ end
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+
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+ def make_required_folders config, sample, index, analysis_folder
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+ super
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+ return unless CagnutPipelineDraw.config_name == config['pipeline_name']
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+ CagnutPipelineDraw::Configuration::Utils.create_output_dirs config, index, analysis_folder
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+ ln_seq_files_to_folder sample, sample['qseq'], sample['fastq']
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+ end
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+
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+ end
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+ end
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+
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+ Cagnut::Configuration::Checks::Datasets.prepend CagnutPipelineDraw::Configuration
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+ module CagnutPipelineDraw
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+ module Pipeline
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+ class Alignment
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+ attr_accessor :bwa, :samtools, :picard, :toolbox
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+
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+ def initialize
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+ @config = Cagnut::Configuration.config
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+ @bwa = ::CagnutBwa::Util.new @config
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+ @samtools = ::CagnutSamtools::Util.new
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+ @picard = ::CagnutPicard::Util.new @config
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+ @toolbox = ::CagnutToolbox::Util.new @config
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+ end
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+
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+ def run order=1
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+ case @config['data_type']
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+ when 'BAM'
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+ puts 'Merging the following bam files'
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+ bam_dir = @config['bam_dir']
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+ puts Dir.entries(bam_dir).select { |f| !File.directory? f }
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+ @samtools.merge_bam samtools_merge_bam_dirs, order
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+ when 'ONEFASTQ', 'ONEFASTQSE'
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+ job_name, order = @bwa.aln_one_fastq bwa_aln_dirs, order
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+ job_name, filename, order = @bwa.samp_one_fastq bwa_samp_dirs, order, job_name
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+ job_name, filename, order = @picard.add_or_replace_readgroups picard_add_read_group_dirs, order, job_name, filename
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+ @samtools.mg_bam_soft_link samtools_mg_bam_soft_link_dirs, order, job_name, filename
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+ else
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+ job_name, filename, order = @toolbox.qseq2fastq toolbox_qseq2fastq_dirs, order
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+ job_name, order = @bwa.aln bwa_aln_dirs, order, job_name, filename
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+ job_name, filename, order = @bwa.samp bwa_samp_dirs, order, job_name, filename
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+ job_name, filename, order = @picard.add_or_replace_readgroups picard_add_read_group_dirs, order, job_name, filename
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+ @samtools.merge_bam samtools_merge_bam_dirs, order, job_name, filename
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+ end
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+ end
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+
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+ private
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+
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+ def toolbox_qseq2fastq_dirs
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+ {
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+ output: @config['sample']['fastq']
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+ }
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+ end
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+
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+ def bwa_samp_dirs
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+ {
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+ input: @config['sample']['sai'],
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+ output: @config['sample']['sam']
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+ }
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+ end
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+
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+ def bwa_aln_dirs
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+ {
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+ output: @config['sample']['sai']
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+ }
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+ end
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+
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+ def samtools_mg_bam_soft_link_dirs
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+ {
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+ input: @config['sample']['bam'],
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+ output: @config['sample']['bam']
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+ }
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+ end
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+
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+ def picard_add_read_group_dirs
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+ {
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+ input: @config['sample']['sam'],
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+ output: @config['sample']['bam'],
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+ tmp_dir: @config['sample']['tmp']
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+ }
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+ end
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+
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+ def samtools_merge_bam_dirs
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+ {
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+ input: @config['sample']['sam'],
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+ output: @config['sample']['bam']
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+ }
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+ end
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+
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+ end
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+ end
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+ end
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+ module CagnutPipelineDraw
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+ module Pipeline
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+ class Recalibration
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+ attr_accessor :gatk, :picard, :samtools
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+
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+ def initialize job_name
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+ @job_name = job_name
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+ @config = Cagnut::Configuration.config
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+ @gatk = ::CagnutGatk::Util.new @config
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+ @picard = ::CagnutPicard::Util.new @config
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+ @samtools = ::CagnutSamtools::Util.new
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+ end
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+
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+ def run filename = nil, order=1
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+ job_name, filename, order = picard.markdup picard_markup_dirs, order, @job_name, filename
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+ order = samtools.do_flag_stat samtools_do_flag_stat_dirs, order, job_name, filename
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+ order = gatk.count_read gatk_count_read_dirs, order, job_name, filename
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+ job_name, filename, order = gatk.recal gatk_recal_dirs, order, job_name, filename
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+ order = picard.picard_qc_metrics picard_picard_qc_metrics_dirs, order, job_name, filename
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+ [job_name, filename, order]
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+ end
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+
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+ private
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+
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+ def picard_markup_dirs
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+ {
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+ input: @config['sample']['bam'],
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+ output: @config['sample']['bam'],
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+ tmp_dir: @config['sample']['tmp']
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+ }
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+ end
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+
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+ def samtools_do_flag_stat_dirs
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+ {
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+ input: @config['sample']['bam'],
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+ output: @config['sample']['stat']
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+ }
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+ end
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+
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+ def gatk_count_read_dirs
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+ {
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+ input: @config['sample']['bam'],
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+ output: @config['sample']['stat']
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+ }
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+ end
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+
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+ def gatk_recal_dirs
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+ {
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+ input: @config['sample']['bam'],
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+ output: @config['sample']['bam'],
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+ contrast: @config['sample']['bam']
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+ }
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+ end
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+
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+ def picard_picard_qc_metrics_dirs
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+ {
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+ input: @config['sample']['bam'],
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+ output: @config['sample']['stat'],
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+ tmp_dir: @config['sample']['tmp']
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+ }
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+ end
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+
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+ end
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+ end
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+ end
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+ module CagnutPipelineDraw
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+ module Pipeline
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+ class VariantCall
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+ attr_accessor :gatk, :snp_eff
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+
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+ def initialize job_name
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+ @job_name = job_name
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+ @config = Cagnut::Configuration.config
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+ @gatk = ::CagnutGatk::Util.new @config
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+ @snpeff = ::CagnutSnpeff::Util.new
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+ end
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+
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+ def run filename = nil, order=1
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+ order = @gatk.depth_of_coverage gatk_depth_of_coverage_dirs, order, @job_name, filename
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+ job_name, filename, order = @gatk.unified_genotyper gatk_unified_genotyper_dirs, order, @job_name, filename
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+ job_name, filename, order = @gatk.snpcal gatk_snpcal_dirs, order, job_name, filename
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+ job_name, order = @snpeff.snp_annotation snpeff_snp_annotation_dirs, order, job_name, filename
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+ # collectSPeekMetrics
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+ [job_name, nil, order+1]
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+ end
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+
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+ private
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+
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+ def gatk_depth_of_coverage_dirs
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+ {
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+ input: @config['sample']['bam'],
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+ output: @config['sample']['stat'],
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+ }
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+ end
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+
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+ def gatk_snpcal_dirs
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+ {
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+ input: @config['sample']['bam'],
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+ output: @config['sample']['vcf'],
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+ }
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+ end
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+
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+ def gatk_unified_genotyper_dirs
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+ {
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+ input: @config['sample']['vcf'],
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+ output: @config['sample']['vcf'],
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+ }
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+ end
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+
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+ def snpeff_snp_annotation_dirs
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+ {
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+ input: @config['sample']['vcf'],
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+ output: @config['sample']['vcf'],
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+ }
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+ end
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+
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+ end
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+ end
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+ end
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+ module CagnutPipelineDraw
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+ VERSION = "0.3.1"
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+ end
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+ bwa:
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+ aln:
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+ params:
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+ - -t 16
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+ samp:
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+ params:
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+ -
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+
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+ gatk:
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+ base_recalibrator:
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+ java:
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+ - -Xmx4g
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+ params:
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+ - -l INFO
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+ - -nct 16
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+ count_reads:
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+ java:
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+ - -Xmx2g
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+ params:
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+ - --read_filter MappingQualityUnavailable
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+ - --read_filter UnmappedRead
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+ - --read_filter DuplicateRead
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+ - --read_filter MappingQualityZero
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+ depth_of_coverage:
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+ java:
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+ - -Xmx5g
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+ params:
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+ - -l INFO
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+ - --summaryCoverageThreshold 10
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+ - --summaryCoverageThreshold 20
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+ indel_realigner:
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+ java:
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+ - -Xmx5g
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+ params:
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+ - --maxReadsInMemory 200000
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+ print_reads:
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+ java:
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+ - -Xmx2g
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+ params:
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+ - -l INFO
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+ - -nct 16
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+ realigner_target_creator:
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+ java:
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+ - -Xmx2g
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+ params:
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+ - -nt 2
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+ unified_genotyper:
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+ java:
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+ - -Xmx4g
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+ params:
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+ - -nt 6
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+ - -mbq 20
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+ - -mmq 30
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+ - -l INFO
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+ - --read_filter MappingQuality
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+ - --read_filter DuplicateRead
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+ - --genotype_likelihoods_model BOTH
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+ variant_eval:
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+ java:
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+ - -Xmx4g
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+ params:
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+ - -EV CountVariants
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+ variant_filtration:
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+ java:
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+ - -Xmx4g
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+ params:
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+ - --clusterWindowSize 10
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+ - --filterName "HomopolymerRun"
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+ - --filterExpression "HRun>=4"
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+ - --filterName "QualByDepth"
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+ - --filterExpression "QD<5.0"
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+ - --filterName "StrandBias"
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+ - --filterExpression "FS>=20.0"
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+ - -l INFO
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+
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+ picard:
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+ add_or_replace_readgroups:
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+ java:
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+ - -Xmx4g
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+ params:
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+ - VALIDATION_STRINGENCY=SILENT
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+ - MAX_RECORDS_IN_RAM=1000000
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+ - SORT_ORDER=coordinate
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+ - CREATE_INDEX=true
85
+ collect_gc_bias_metrics:
86
+ java:
87
+ - -Xmx2g
88
+ params:
89
+ - VALIDATION_STRINGENCY=SILENT
90
+ collect_insert_size_metrics:
91
+ java:
92
+ - -Xmx2g
93
+ params:
94
+ - VALIDATION_STRINGENCY=SILENT
95
+ markduplicate:
96
+ java:
97
+ - -Xmx4g
98
+ params:
99
+ - VALIDATION_STRINGENCY=SILENT
100
+ - REMOVE_DUPLICATES=false
101
+ - CREATE_INDEX=true
102
+ - METRICS_FILE=metrics
103
+ - MAX_RECORDS_IN_RAM=1000000
104
+ - OPTICAL_DUPLICATE_PIXEL_DISTANCE=10
105
+ mean_quality_by_cycle:
106
+ java:
107
+ - -Xmx2g
108
+ params:
109
+ - ALIGNED_READS_ONLY=TRUE
110
+ - VALIDATION_STRINGENCY=SILENT
111
+ - PF_READS_ONLY=TRUE
112
+ quailty_score_distribution:
113
+ java:
114
+ - -Xmx2g
115
+ params:
116
+ - VALIDATION_STRINGENCY=SILENT
117
+ - ALIGNED_READS_ONLY=TRUE
118
+ - PF_READS_ONLY=TRUE
119
+
120
+ samtools:
121
+ do_flag_stat:
122
+ params:
123
+ -
124
+ merge_bam:
125
+ params:
126
+ -
127
+ mg_Bam_soft_link:
128
+ params:
129
+ -
130
+
131
+ snpeff:
132
+ annotation:
133
+ java:
134
+ - -Xmx4g
135
+ params:
136
+ - -i VCF
137
+ - -o VCF
138
+
139
+ toolbox:
140
+ qseq_to_fastq:
141
+ params:
142
+ -
metadata ADDED
@@ -0,0 +1,206 @@
1
+ --- !ruby/object:Gem::Specification
2
+ name: cagnut_pipeline_draw
3
+ version: !ruby/object:Gem::Version
4
+ version: 0.3.1
5
+ platform: ruby
6
+ authors:
7
+ - Shi-Gang Wang
8
+ - Tse-Ching Ho
9
+ autorequire:
10
+ bindir: exe
11
+ cert_chain: []
12
+ date: 2016-12-01 00:00:00.000000000 Z
13
+ dependencies:
14
+ - !ruby/object:Gem::Dependency
15
+ name: cagnut_core
16
+ requirement: !ruby/object:Gem::Requirement
17
+ requirements:
18
+ - - ">="
19
+ - !ruby/object:Gem::Version
20
+ version: '0'
21
+ type: :runtime
22
+ prerelease: false
23
+ version_requirements: !ruby/object:Gem::Requirement
24
+ requirements:
25
+ - - ">="
26
+ - !ruby/object:Gem::Version
27
+ version: '0'
28
+ - !ruby/object:Gem::Dependency
29
+ name: cagnut_bwa
30
+ requirement: !ruby/object:Gem::Requirement
31
+ requirements:
32
+ - - ">="
33
+ - !ruby/object:Gem::Version
34
+ version: '0'
35
+ type: :runtime
36
+ prerelease: false
37
+ version_requirements: !ruby/object:Gem::Requirement
38
+ requirements:
39
+ - - ">="
40
+ - !ruby/object:Gem::Version
41
+ version: '0'
42
+ - !ruby/object:Gem::Dependency
43
+ name: cagnut_gatk
44
+ requirement: !ruby/object:Gem::Requirement
45
+ requirements:
46
+ - - ">="
47
+ - !ruby/object:Gem::Version
48
+ version: '0'
49
+ type: :runtime
50
+ prerelease: false
51
+ version_requirements: !ruby/object:Gem::Requirement
52
+ requirements:
53
+ - - ">="
54
+ - !ruby/object:Gem::Version
55
+ version: '0'
56
+ - !ruby/object:Gem::Dependency
57
+ name: cagnut_samtools
58
+ requirement: !ruby/object:Gem::Requirement
59
+ requirements:
60
+ - - ">="
61
+ - !ruby/object:Gem::Version
62
+ version: '0'
63
+ type: :runtime
64
+ prerelease: false
65
+ version_requirements: !ruby/object:Gem::Requirement
66
+ requirements:
67
+ - - ">="
68
+ - !ruby/object:Gem::Version
69
+ version: '0'
70
+ - !ruby/object:Gem::Dependency
71
+ name: cagnut_picard
72
+ requirement: !ruby/object:Gem::Requirement
73
+ requirements:
74
+ - - ">="
75
+ - !ruby/object:Gem::Version
76
+ version: '0'
77
+ type: :runtime
78
+ prerelease: false
79
+ version_requirements: !ruby/object:Gem::Requirement
80
+ requirements:
81
+ - - ">="
82
+ - !ruby/object:Gem::Version
83
+ version: '0'
84
+ - !ruby/object:Gem::Dependency
85
+ name: cagnut_snpeff
86
+ requirement: !ruby/object:Gem::Requirement
87
+ requirements:
88
+ - - ">="
89
+ - !ruby/object:Gem::Version
90
+ version: '0'
91
+ type: :runtime
92
+ prerelease: false
93
+ version_requirements: !ruby/object:Gem::Requirement
94
+ requirements:
95
+ - - ">="
96
+ - !ruby/object:Gem::Version
97
+ version: '0'
98
+ - !ruby/object:Gem::Dependency
99
+ name: cagnut_toolbox
100
+ requirement: !ruby/object:Gem::Requirement
101
+ requirements:
102
+ - - ">="
103
+ - !ruby/object:Gem::Version
104
+ version: '0'
105
+ type: :runtime
106
+ prerelease: false
107
+ version_requirements: !ruby/object:Gem::Requirement
108
+ requirements:
109
+ - - ">="
110
+ - !ruby/object:Gem::Version
111
+ version: '0'
112
+ - !ruby/object:Gem::Dependency
113
+ name: bundler
114
+ requirement: !ruby/object:Gem::Requirement
115
+ requirements:
116
+ - - "~>"
117
+ - !ruby/object:Gem::Version
118
+ version: '1.12'
119
+ type: :development
120
+ prerelease: false
121
+ version_requirements: !ruby/object:Gem::Requirement
122
+ requirements:
123
+ - - "~>"
124
+ - !ruby/object:Gem::Version
125
+ version: '1.12'
126
+ - !ruby/object:Gem::Dependency
127
+ name: rake
128
+ requirement: !ruby/object:Gem::Requirement
129
+ requirements:
130
+ - - "~>"
131
+ - !ruby/object:Gem::Version
132
+ version: '10.0'
133
+ type: :development
134
+ prerelease: false
135
+ version_requirements: !ruby/object:Gem::Requirement
136
+ requirements:
137
+ - - "~>"
138
+ - !ruby/object:Gem::Version
139
+ version: '10.0'
140
+ - !ruby/object:Gem::Dependency
141
+ name: rspec
142
+ requirement: !ruby/object:Gem::Requirement
143
+ requirements:
144
+ - - "~>"
145
+ - !ruby/object:Gem::Version
146
+ version: '3.0'
147
+ type: :development
148
+ prerelease: false
149
+ version_requirements: !ruby/object:Gem::Requirement
150
+ requirements:
151
+ - - "~>"
152
+ - !ruby/object:Gem::Version
153
+ version: '3.0'
154
+ description: Cagnut Draw Pipeline
155
+ email:
156
+ - seanwang@goldenio.com
157
+ - tsechingho@goldenio.com
158
+ executables: []
159
+ extensions: []
160
+ extra_rdoc_files: []
161
+ files:
162
+ - ".gitignore"
163
+ - ".rspec"
164
+ - ".ruby-version"
165
+ - ".travis.yml"
166
+ - Gemfile
167
+ - LICENSE.txt
168
+ - README.md
169
+ - Rakefile
170
+ - bin/console
171
+ - bin/setup
172
+ - cagnut_pipeline_draw.gemspec
173
+ - lib/cagnut_pipeline_draw.rb
174
+ - lib/cagnut_pipeline_draw/cli/new_project/draw.rb
175
+ - lib/cagnut_pipeline_draw/cli/pipeline/draw.rb
176
+ - lib/cagnut_pipeline_draw/configuration.rb
177
+ - lib/cagnut_pipeline_draw/pipeline/alignment.rb
178
+ - lib/cagnut_pipeline_draw/pipeline/recalibration.rb
179
+ - lib/cagnut_pipeline_draw/pipeline/variant_call.rb
180
+ - lib/cagnut_pipeline_draw/version.rb
181
+ - templates/draw_tools.yml
182
+ homepage: https://github.com/CAGNUT/cagnut_pipeline_draw
183
+ licenses:
184
+ - MIT
185
+ metadata: {}
186
+ post_install_message:
187
+ rdoc_options: []
188
+ require_paths:
189
+ - lib
190
+ required_ruby_version: !ruby/object:Gem::Requirement
191
+ requirements:
192
+ - - ">="
193
+ - !ruby/object:Gem::Version
194
+ version: '0'
195
+ required_rubygems_version: !ruby/object:Gem::Requirement
196
+ requirements:
197
+ - - ">="
198
+ - !ruby/object:Gem::Version
199
+ version: '0'
200
+ requirements: []
201
+ rubyforge_project:
202
+ rubygems_version: 2.5.1
203
+ signing_key:
204
+ specification_version: 4
205
+ summary: Cagnut Draw Pipeline
206
+ test_files: []