cagnut_picard 0.3.0

checksums.yaml

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+---
+SHA1:
+  metadata.gz: b1a0e031d3539d0901778f55ecc65ce135909878
+  data.tar.gz: 8f2eb71e9cef1eb0f9ee98a7012d3ae965ec6c1d
+SHA512:
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data/.gitignore

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+/.bundle/
+/.yardoc
+/Gemfile.lock
+/_yardoc/
+/coverage/
+/doc/
+/pkg/
+/spec/reports/
+/tmp/

data/.rspec

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+--format documentation
+--color

data/.ruby-version

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+ruby-2.3.1

data/.travis.yml

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+sudo: false
+language: ruby
+rvm:
+  - 2.3.1
+before_install: gem install bundler -v 1.12.5

data/Gemfile

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+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in cagnut_picard.gemspec
+gemspec

data/LICENSE.txt

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+The MIT License (MIT)
+
+Copyright (c) 2016 Goldenio Technology
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

data/README.md

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+# CagnutPicard
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+```ruby
+gem 'cagnut_picard'
+```
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install cagnut_picard
+
+## Usage
+
+## Development
+
+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.
+
+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).
+
+## Contributing
+
+Bug reports and pull requests are welcome on GitHub at https://github.com/[USERNAME]/cagnut_picard.
+
+
+## License
+
+The gem is available as open source under the terms of the [MIT License](http://opensource.org/licenses/MIT).
+

data/Rakefile

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+require "bundler/gem_tasks"
+require "rspec/core/rake_task"
+
+RSpec::Core::RakeTask.new(:spec)
+
+task :default => :spec

data/bin/console

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+#!/usr/bin/env ruby
+
+require "bundler/setup"
+require "cagnut_picard"
+
+# You can add fixtures and/or initialization code here to make experimenting
+# with your gem easier. You can also use a different console, if you like.
+
+# (If you use this, don't forget to add pry to your Gemfile!)
+# require "pry"
+# Pry.start
+
+require "irb"
+IRB.start

data/bin/setup

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+#!/usr/bin/env bash
+set -euo pipefail
+IFS=$'\n\t'
+set -vx
+
+bundle install
+
+# Do any other automated setup that you need to do here

data/cagnut_picard.gemspec

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+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'cagnut_picard/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "cagnut_picard"
+  spec.version       = CagnutPicard::VERSION
+  spec.authors       = ['Shi-Gang Wang', 'Tse-Ching Ho']
+  spec.email         = ['seanwang@goldenio.com', 'tsechingho@goldenio.com']
+
+  spec.summary       = %q{Cagnut Picard tools}
+  spec.description   = %q{Cagnut Picard tools}
+  spec.homepage      = "https://github.com/CAGNUT/cagnut_picard"
+  spec.license       = "MIT"
+
+  spec.files         = `git ls-files -z`.split("\x0").reject { |f| f.match(%r{^(test|spec|features)/}) }
+  spec.bindir        = "exe"
+  spec.executables   = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
+  spec.require_paths = ["lib"]
+
+  spec.add_dependency 'cagnut_core'
+
+  spec.add_development_dependency "bundler", "~> 1.12"
+  spec.add_development_dependency "rake", "~> 10.0"
+  spec.add_development_dependency "rspec", "~> 3.0"
+end

data/lib/cagnut_picard/base.rb

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+require 'cagnut_picard/functions/add_or_replace_readgroups'
+require 'cagnut_picard/functions/markdup'
+require 'cagnut_picard/functions/build_bam_index'
+require 'cagnut_picard/functions/mean_quality_by_cycle'
+require 'cagnut_picard/functions/quality_score_distribution'
+require 'cagnut_picard/functions/collect_gc_bias_metrics'
+require 'cagnut_picard/functions/collect_insert_size_metrics'
+require 'cagnut_picard/functions/sort_sam'
+require 'cagnut_picard/functions/collect_multiple_metrics'
+
+
+module CagnutPicard
+  class Base
+    def add_or_replace_readgroups dirs, order, previous_job_id = nil, input = nil
+      opts = { input: input, dirs: dirs, order: order }
+      CagnutPicard::AddOrReplaceReadGroups.new(opts).run previous_job_id
+    end
+
+    def markdup dirs, order, previous_job_id, input = nil
+      opts = { input: input, dirs: dirs, order: order }
+      CagnutPicard::Markdup.new(opts).run previous_job_id
+    end
+
+    def build_bam_index dirs, order, previous_job_id, input
+      opts = { input: input, dirs: dirs, order: order }
+      CagnutPicard::BuildBamIndex.new(opts).run previous_job_id
+    end
+
+    def mean_quality_by_cycle dirs, order, previous_job_id, input
+      opts = { input: input, dirs: dirs, order: order }
+      CagnutPicard::MeanQualityByCycle.new(opts).run previous_job_id
+    end
+
+    def quality_score_distribution dirs, order, previous_job_id, input
+      opts = { input: input, dirs: dirs, order: order }
+      CagnutPicard::QualityScoreDistribution.new(opts).run previous_job_id
+    end
+
+    def collect_gc_bias_metrics dirs, order, previous_job_id, input
+      opts = { input: input, dirs: dirs, order: order }
+      CagnutPicard::CollectGcBiasMetrics.new(opts).run previous_job_id
+    end
+
+    def collect_insert_size_metrics dirs, order, previous_job_id, input
+      opts = { input: input, dirs: dirs, order: order }
+      CagnutPicard::CollectInsertSizeMetrics.new(opts).run previous_job_id
+    end
+
+    def sort_sam dirs, order, previous_job_id, input = nil
+      opts = { input: input, dirs: dirs, order: order }
+      CagnutPicard::SortSam.new(opts).run previous_job_id
+    end
+
+    def collect_multiple_metrics dirs, order, previous_job_id, input
+      opts = { input: input, dirs: dirs, order: order }
+      CagnutPicard::CollectMultipleMetrics.new(opts).run previous_job_id
+    end
+  end
+end

data/lib/cagnut_picard/check_tools.rb

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+module CagnutPicard
+  module CheckTools
+    def check_tool tools_path
+      super if defined?(super)
+      check_Picard tools_path['Picard'] if @java
+      check_picard_dict refs['ref_fasta']
+    end
+
+    def check_Picard path
+      check_tool_ver 'Picard' do
+        `#{@java} -jar #{path} AddOrReplaceReadGroups --version 2>&1` if path
+      end
+    end
+
+    def check_picard_dict ref_path
+      tool = 'Sequence Dictionary'
+      file = ref_path.gsub '.fasta', '.dict'
+      command =
+        "#{@java} -jar #{@config['tools']['picard']} CreateSequenceDictionary REFERENCE=#{ref_path} OUTPUT=#{file}"
+      check_ref_related file, tool, command
+    end
+
+    def check_ref_related file, tool, command
+      if File.exist?(file)
+        puts "\t#{tool}: Done"
+      else
+        puts "\t#{tool}: Not Found!"
+        puts "\tPlease execute command:"
+        puts "\t\t#{command}"
+        @check_completed = false
+      end
+    end
+  end
+end
+
+Cagnut::Configuration::Checks::Tools.prepend CagnutPicard::CheckTools

data/lib/cagnut_picard/configuration.rb

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+require 'singleton'
+
+module CagnutPicard
+  class Configuration
+    include Singleton
+    attr_accessor :rg_str_picard, :add_or_replace_readgroups_params, :sort_sam_params,
+                  :build_bam_index_params, :quailty_score_distribution_params,
+                  :collect_gc_bias_metrics_params, :collect_insert_size_metrics_params,
+                  :collect_multiple_metrics_params, :markduplicate_params,
+                  :mean_quality_by_cycle_params
+
+    class << self
+      def load config, params
+        instance.load config, params
+      end
+    end
+
+    def load config, params
+      @config = config
+      @params = params
+      generate_rg_str
+      attributes.each do |name, value|
+        send "#{name}=", value if respond_to? "#{name}="
+      end
+    end
+
+    def attributes
+      {
+        rg_str_picard: @config['sample']['rg_str_picard'],
+        add_or_replace_readgroups_params: add_java_params(@params['add_or_replace_readgroups'], true),
+        build_bam_index_params: add_java_params(@params['build_bam_index']),
+        collect_gc_bias_metrics_params: add_java_params(@params['collect_gc_bias_metrics']),
+        collect_insert_size_metrics_params: add_java_params(@params['collect_insert_size_metrics']),
+        collect_multiple_metrics_params: add_java_params(@params['collect_multiple_metrics']),
+        markduplicate_params: add_java_params(@params['markduplicate']),
+        mean_quality_by_cycle_params: add_java_params(@params['mean_quality_by_cycle']),
+        quailty_score_distribution_params: add_java_params(@params['quailty_score_distribution']),
+        sort_sam_params: add_java_params(@params['sort_sam'])
+      }
+    end
+
+    def add_java_params method_params, verbose=false
+      return if method_params.blank?
+      array = method_params['java'].dup
+      array << "-verbose:sizes" if verbose
+      array << "-jar #{@config['tools']['picard']}"
+      {
+        'java' => array,
+        'params' => method_params['params']
+      }
+    end
+
+    def generate_rg_str
+      @config['samples'].each do |sample|
+        arg = %W(
+          ID=#{sample['rgid']}
+          SM=#{sample['name']}
+          PL=#{@config['info']['pl']}
+          PU=#{sample['pu']}
+          LB=#{@config['info']['lb']}
+          DS=#{@config['info']['ds']}
+          CN=#{@config['info']['cn']}
+        )
+        rg_str_picard = { 'rg_str_picard' => arg.join(' ') }
+        sample.merge! rg_str_picard
+      end
+
+    end
+  end
+end

data/lib/cagnut_picard/functions/add_or_replace_readgroups.rb

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+module CagnutPicard
+  class AddOrReplaceReadGroups
+    extend Forwardable
+
+    def_delegators :'Cagnut::Configuration.base', :sample_name, :dodebug,
+                   :jobs_dir, :magic28, :prefix_name, :ref_fasta, :java_path
+    def_delegators :'CagnutPicard.config', :rg_str_picard, :add_or_replace_readgroups_params
+
+    def initialize opts = {}
+      @order = sprintf '%02i', opts[:order]
+      @tmp_dir = opts[:dirs][:tmp_dir]
+      @input = opts[:input].nil? ? "#{opts[:dirs][:input]}/#{sample_name}_aligned.sam.gz" : opts[:input]
+      @output = "#{opts[:dirs][:output]}/#{sample_name}.bam"
+      @job_name = "#{prefix_name}_addRG_#{sample_name}_addrg"
+    end
+
+    def run previous_job_id = nil
+      puts "Submitting addReadGroup #{sample_name}"
+      script_name = generate_script
+      ::Cagnut::JobManage.submit script_name, @job_name, queuing_options(previous_job_id)
+      [@job_name, @output]
+    end
+
+    def queuing_options previous_job_id = nil
+      {
+        previous_job_id: previous_job_id,
+        adjust_memory: ['h_vmem=10G'],
+        tools: ['picard', 'add_or_replace_readgroups']
+      }
+    end
+
+    def add_read_group_options
+      array = add_or_replace_readgroups_params['params'].dup
+      array << "INPUT=#{@input}"
+      array << "OUTPUT=#{@output}"
+      array << "TMP_DIR=#{@tmp_dir} "
+      array << "#{rg_str_picard}"
+      array.uniq
+    end
+
+    def modified_java_array
+      array = add_or_replace_readgroups_params['java'].dup
+      array << 'AddOrReplaceReadGroups'
+      array.unshift(java_path).uniq
+    end
+
+    def params_combination_hash
+      @params_combination_hash ||= {
+        'java' => modified_java_array,
+        'params' => add_read_group_options
+      }
+    end
+
+    def generate_script
+      script_name = "#{@order}_picard_add_or_replace_readgroups"
+      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 $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"
+          #{params_combination_hash['java'].join("\s")} \\
+            #{params_combination_hash['params'].join(" \\\n            ")} \\
+            #{::Cagnut::JobManage.run_local}
+
+          EXITSTATUS=$?
+
+          if [ ! -e "#{@output}" ]
+          then
+            echo "Missing output: #{@output}"
+            exit 100
+          fi
+
+          # Check BAM EOF
+          BAM_28=$(tail -c 28 #{@output}|xxd -p)
+          if [ '#{magic28}' != "$BAM_28" ]
+          then
+            echo "Error with BAM EOF" 1>&2
+            exit 100
+          fi
+
+          if [ $EXITSTATUS -ne 0 ];then exit $EXITSTATUS;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
+  end
+end

data/lib/cagnut_picard/functions/build_bam_index.rb

@@ -0,0 +1,74 @@
+module CagnutPicard
+  class BuildBamIndex
+    extend Forwardable
+
+    def_delegators :'Cagnut::Configuration.base', :sample_name, :prefix_name,
+                   :jobs_dir, :dodebug, :java_path
+    def_delegators :'CagnutPicard.config', :build_bam_index_params
+
+    def initialize opts = {}
+      @order = sprintf '%02i', opts[:order]
+      @job_name = "#{prefix_name}_build_bam_index_#{sample_name}"
+      @input = opts[:input].nil? ? "#{opts[:dirs][:input]}/#{sample_name}_markdup.bam" : opts[:input]
+    end
+
+    def run previous_job_id = nil
+      puts "Submitting build_bam_index #{sample_name}"
+      script_name = generate_script
+      ::Cagnut::JobManage.submit script_name, @job_name, queuing_options(previous_job_id)
+      @job_name
+    end
+
+    def queuing_options previous_job_id = nil
+      {
+        previous_job_id: previous_job_id,
+        adjust_memory: ['h_vmem=10G'],
+        tools: ['picard', 'build_bam_index']
+      }
+    end
+
+    def build_bam_index_options
+      array = build_bam_index_params['params'].dup
+      array << "I=#{@input}"
+      array.uniq.compact
+    end
+
+    def modified_java_array
+      array = build_bam_index_params['java'].dup
+      array << 'BuildBamIndex'
+      array.unshift(java_path).uniq
+    end
+
+    def params_combination_hash
+      @params_combination_hash ||= {
+        'java' => modified_java_array,
+        'params' => build_bam_index_options
+      }
+    end
+
+    def generate_script
+      script_name = "#{@order}_picard_build_bam_index"
+      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 $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"
+          #{params_combination_hash['java'].join("\s")} \\
+            #{params_combination_hash['params'].join(" \\\n            ")} \\
+            #{::Cagnut::JobManage.run_local}
+
+          EXITSTATUS=$?
+
+          if [ $EXITSTATUS -ne 0 ];then exit $EXITSTATUS;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
+  end
+end

data/lib/cagnut_picard/functions/collect_gc_bias_metrics.rb

@@ -0,0 +1,82 @@
+module CagnutPicard
+  class CollectGcBiasMetrics
+    extend Forwardable
+
+    def_delegators :'Cagnut::Configuration.base', :sample_name, :jobs_dir, :dodebug,
+                   :ref_fasta, :prefix_name, :java_path
+    def_delegators :'CagnutPicard.config', :collect_gc_bias_metrics_params
+
+    def initialize opts = {}
+      @order = sprintf '%02i', opts[:order]
+      @tmp_dir = opts[:dirs][:tmp_dir]
+      @job_name = "#{prefix_name}_collect_gc_bias_metrics_#{sample_name}"
+      @input = opts[:input].nil? ? "#{opts[:dirs][:input]}/#{sample_name}_recal.bam" : opts[:input]
+      @output = "#{opts[:dirs][:output]}/Gc_Bias_Metrics"
+      @chart_output = "#{opts[:dirs][:output]}/Gc_bias_#{sample_name}.pdf"
+      @summary_output = "#{opts[:dirs][:output]}/sum_out_gc"
+    end
+
+    def run previous_job_id = nil
+      puts "Submitting Picard CollectGcBiasMetrics #{sample_name} Jobs "
+      script_name = generate_script
+      ::Cagnut::JobManage.submit script_name, @job_name, queuing_options(previous_job_id)
+      @job_name
+    end
+
+    def queuing_options previous_job_id = nil
+      {
+        previous_job_id: previous_job_id,
+        adjust_memory: ['h_vmem=5G'],
+        tools: ['picard', 'collect_gc_bias_metrics']
+      }
+    end
+
+    def collect_gc_bias_metrics_options
+      array = collect_gc_bias_metrics_params['params'].dup
+      array << "REFERENCE_SEQUENCE=#{ref_fasta}"
+      array << "TMP_DIR=#{@tmp_dir}"
+      array << "INPUT=#{@input}"
+      array << "OUTPUT=#{@output}"
+      array << "CHART_OUTPUT=#{@chart_output}"
+      array << "SUMMARY_OUTPUT=#{@summary_output}"
+      array.uniq
+    end
+
+    def modified_java_array
+      array = collect_gc_bias_metrics_params['java'].dup
+      array << 'CollectGcBiasMetrics'
+      array.unshift(java_path).uniq
+    end
+
+    def params_combination_hash
+      @params_combination_hash ||= {
+        'java' => modified_java_array,
+        'params' => collect_gc_bias_metrics_options
+      }
+    end
+
+    def generate_script
+      script_name = "#{@order}_picard_collect_gc_bias_metrics"
+      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 $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"
+          #{params_combination_hash['java'].join("\s")} \\
+            #{params_combination_hash['params'].join(" \\\n            ")} \\
+            #{::Cagnut::JobManage.run_local}
+
+          EXITSTATUS=$?
+          if [ ! -s "#{@chart_output}" ]; then 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
+  end
+end

data/lib/cagnut_picard/functions/collect_insert_size_metrics.rb

@@ -0,0 +1,81 @@
+module CagnutPicard
+  class CollectInsertSizeMetrics
+    extend Forwardable
+
+    def_delegators :'Cagnut::Configuration.base', :sample_name, :dodebug,
+                   :ref_fasta, :prefix_name, :jobs_dir, :java_path
+    def_delegators :'CagnutPicard.config', :collect_insert_size_metrics_params
+
+    def initialize opts = {}
+      @order = sprintf '%02i', opts[:order]
+      @tmp_dir = opts[:dirs][:tmp_dir]
+      @job_name = "#{prefix_name}_insertSize_#{sample_name}"
+      @input = opts[:input].nil? ? "#{opts[:dirs][:input]}/#{sample_name}_recal.bam" : opts[:input]
+      @output = "#{opts[:dirs][:output]}/Metric_file"
+      @histogram_file = "#{opts[:dirs][:output]}/hst_Insert_#{sample_name}.pdf"
+    end
+
+    def run previous_job_id = nil
+      puts "Submitting Picard CollectInsertSizeMetrics #{sample_name} Jobs"
+      script_name = generate_script
+      ::Cagnut::JobManage.submit script_name, @job_name, queuing_options(previous_job_id)
+      @job_name
+    end
+
+    def queuing_options previous_job_id = nil
+      {
+        previous_job_id: previous_job_id,
+        adjust_memory: ['h_vmem=5G'],
+        tools: ['picard', 'collect_insert_size_metrics']
+      }
+    end
+
+    def collect_insert_size_metrics_options
+      array = collect_insert_size_metrics_params['params'].dup
+      array << "INPUT=#{@input}"
+      array << "OUTPUT=#{@output}"
+      array << "TMP_DIR=#{@tmp_dir}"
+      array << "HISTOGRAM_FILE=#{@histogram_file}"
+      array.uniq
+    end
+
+    def modified_java_array
+      array = collect_insert_size_metrics_params['java'].dup
+      array << 'CollectInsertSizeMetrics'
+      array.unshift(java_path).uniq
+    end
+
+    def params_combination_hash
+      @params_combination_hash ||= {
+        'java' => modified_java_array,
+        'params' => collect_insert_size_metrics_options
+      }
+    end
+
+    def generate_script
+      script_name = "#{@order}_picard_collect_insert_size_metrics"
+      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 $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"
+          #{params_combination_hash['java'].join("\s")} \\
+            #{params_combination_hash['params'].join(" \\\n            ")} \\
+            #{::Cagnut::JobManage.run_local}
+
+          EXITSTATUS=$?
+
+          #if [ ! -s "#{@histogram_file}" ]; then 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
+  end
+end

data/lib/cagnut_picard/functions/collect_multiple_metrics.rb

@@ -0,0 +1,79 @@
+module CagnutPicard
+  class CollectMultipleMetrics
+    extend Forwardable
+
+    def_delegators :'Cagnut::Configuration.base', :sample_name, :dodebug, :prefix_name,
+                   :jobs_dir, :magic28, :java_path, :ref_fasta
+    def_delegators :'CagnutPicard.config', :rg_str_picard, :collect_multiple_metrics_params
+
+    def initialize opts = {}
+      @order = sprintf '%02i', opts[:order]
+      @input = opts[:input].nil? ? "#{opts[:dirs][:input]}/#{sample_name}_recal.bam" : opts[:input]
+      @output = "#{opts[:dirs][:output]}/#{sample_name}_multiple_metrics"
+      @job_name = "#{prefix_name}_CollectMultipleMetrics_#{sample_name}"
+    end
+
+    def run previous_job_id = nil
+      puts "Submitting CollectMultipleMetrics #{sample_name}"
+      script_name = generate_script
+      ::Cagnut::JobManage.submit script_name, @job_name, queuing_options(previous_job_id)
+      @job_name
+    end
+
+    def queuing_options previous_job_id = nil
+      {
+        previous_job_id: previous_job_id,
+        var_env: [rg_str_picard],
+        adjust_memory: ['h_vmem=10G'],
+        tools: ['picard', 'collect_multiple_metrics']
+      }
+    end
+
+    def collect_multiple_metrics_options
+      array = collect_multiple_metrics_params['params'].dup
+      array << "REFERENCE_SEQUENCE=#{ref_fasta}"
+      array << "I=#{@input}"
+      array << "O=#{@output}"
+      array.uniq
+
+    end
+
+    def modified_java_array
+      array = collect_multiple_metrics_params['java'].dup
+      array << 'CollectMultipleMetrics'
+      array.unshift(java_path).uniq
+    end
+
+    def params_combination_hash
+      @params_combination_hash ||= {
+        'java' => modified_java_array,
+        'params' => collect_multiple_metrics_options
+      }
+    end
+
+    def generate_script
+      script_name = "#{@order}_picard_collect_multiple_metrics"
+      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 $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"
+          #{params_combination_hash['java'].join("\s")} \\
+            #{params_combination_hash['params'].join(" \\\n            ")} \\
+            #{::Cagnut::JobManage.run_local}
+
+          EXITSTATUS=$?
+
+          if [ $EXITSTATUS -ne 0 ];then exit $EXITSTATUS;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
+  end
+end

data/lib/cagnut_picard/functions/markdup.rb

@@ -0,0 +1,92 @@
+module CagnutPicard
+  class Markdup
+    extend Forwardable
+
+    def_delegators :'Cagnut::Configuration.base', :jobs_dir, :magic28,
+                   :sample_name, :java_path, :ref_fasta, :prefix_name, :dodebug
+    def_delegators :'CagnutPicard.config', :markduplicate_params
+
+    def initialize opts = {}
+      @order = sprintf '%02i', opts[:order]
+      @tmp_dir = opts[:dirs][:tmp_dir]
+      @job_name = "#{prefix_name}_markdup_#{sample_name}"
+      @input = opts[:input].nil? ? "#{opts[:dirs][:input]}/#{sample_name}_merged.bam" : opts[:input]
+      @output = "#{opts[:dirs][:output]}/#{sample_name}_markdup.bam"
+    end
+
+    def run previous_job_id = nil
+      puts "Submitting markdup #{sample_name}"
+      script_name = generate_script
+      ::Cagnut::JobManage.submit script_name, @job_name, queuing_options(previous_job_id)
+      [@job_name, @output]
+    end
+
+    def queuing_options previous_job_id = nil
+      {
+        previous_job_id: previous_job_id,
+        adjust_memory: ['h_vmem=5G'],
+        tools: ['picard', 'markduplicate']
+      }
+    end
+
+    def markduplicate_options
+      array = markduplicate_params['params'].dup
+      array << "INPUT=#{@input}"
+      array << "OUTPUT=#{@output}"
+      array << "TMP_DIR=#{@tmp_dir}"
+      array.uniq
+    end
+
+    def modified_java_array
+      array = markduplicate_params['java'].dup
+      array << 'MarkDuplicates'
+      array.unshift(java_path).uniq
+    end
+
+    def params_combination_hash
+      @params_combination_hash ||= {
+        'java' => modified_java_array,
+        'params' => markduplicate_options
+      }
+    end
+
+    def generate_script
+      script_name = "#{@order}_picard_markdup"
+      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 $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"
+          #{params_combination_hash['java'].join("\s")} \\
+            #{params_combination_hash['params'].join(" \\\n            ")} \\
+            #{::Cagnut::JobManage.run_local}
+
+          EXITSTATUS=$?
+
+          if [ ! -e "#{@output}" ]
+          then
+            echo "Missing output: #{@output}"
+            exit 100
+          fi
+
+          # Check BAM EOF
+          BAM_28=$(tail -c 28 #{@output}|xxd -p)
+          if [ "#{magic28}" != "$BAM_28" ]
+          then
+            echo "Error with BAM EOF" 1>&2
+            exit 100
+          fi
+
+          if [ $EXITSTATUS -ne 0 ];then exit $EXITSTATUS;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
+  end
+end

data/lib/cagnut_picard/functions/mean_quality_by_cycle.rb

@@ -0,0 +1,79 @@
+module CagnutPicard
+  class MeanQualityByCycle
+    extend Forwardable
+
+    def_delegators :'Cagnut::Configuration.base', :sample_name, :jobs_dir, :java_path,
+                   :ref_fasta, :prefix_name, :dodebug
+    def_delegators :'CagnutPicard.config', :mean_quality_by_cycle_params
+
+    def initialize opts = {}
+      @order = sprintf '%02i', opts[:order]
+      @tmp_dir = opts[:dirs][:tmp_dir]
+      @job_name = "#{prefix_name}_meanQbycycle_#{sample_name}"
+      @input = opts[:input].nil? ? "#{opts[:dirs][:input]}/#{sample_name}_recal.bam" : opts[:input]
+      @output = "#{opts[:dirs][:output]}/quality_table"
+      @chart_output= "#{opts[:dirs][:output]}/qualityByCycle_#{sample_name}.pdf"
+    end
+
+    def run previous_job_id = nil
+      puts "Submitting Picard MeanQualityByCycle #{sample_name} Jobs"
+      script_name = generate_script
+      ::Cagnut::JobManage.submit script_name, @job_name, queuing_options(previous_job_id)
+      @job_name
+    end
+
+    def queuing_options previous_job_id = nil
+      {
+        previous_job_id: previous_job_id,
+        adjust_memory: ['h_vmem=5G'],
+        tools: ['picard', 'mean_quality_by_cycle']
+      }
+    end
+
+    def mean_quality_by_cycle_options
+      array = mean_quality_by_cycle_params['params'].dup
+      array << "INPUT=#{@input}"
+      array << "OUTPUT=#{@output}"
+      array << "TMP_DIR=#{@tmp_dir}"
+      array << "CHART_OUTPUT=#{@chart_output}"
+      array.uniq
+    end
+
+    def modified_java_array
+      array = mean_quality_by_cycle_params['java'].dup
+      array << 'MeanQualityByCycle'
+      array.unshift(java_path).uniq
+    end
+
+    def params_combination_hash
+      @params_combination_hash ||= {
+        'java' => modified_java_array,
+        'params' => mean_quality_by_cycle_options
+      }
+    end
+
+    def generate_script
+      script_name = "#{@order}_picard_meanQbycycle"
+      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 $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"
+          #{params_combination_hash['java'].join("\s")} \\
+            #{params_combination_hash['params'].join(" \\\n            ")} \\
+            #{::Cagnut::JobManage.run_local}
+
+          EXITSTATUS=$?
+          if [ ! -s "#{@chart_output}" ]; then 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
+  end
+end

data/lib/cagnut_picard/functions/quality_score_distribution.rb

@@ -0,0 +1,79 @@
+module CagnutPicard
+  class QualityScoreDistribution
+    extend Forwardable
+
+    def_delegators :'Cagnut::Configuration.base', :sample_name, :jobs_dir, :java_path,
+                   :ref_fasta, :prefix_name, :dodebug
+    def_delegators :'CagnutPicard.config', :quailty_score_distribution_params
+
+    def initialize opts = {}
+      @order = sprintf '%02i', opts[:order]
+      @tmp = opts[:dirs][:tmp_dir]
+      @job_name = "#{prefix_name}_meanQScDis_#{sample_name}"
+      @input = opts[:input].nil? ? "#{opts[:dirs][:input]}/#{sample_name}_recal.bam" : opts[:input]
+      @output = "#{opts[:dirs][:output]}/quality_table"
+      @chart_output = "#{opts[:dirs][:output]}/quality_filter_score_#{sample_name}.pdf"
+    end
+
+    def run previous_job_id = nil
+      puts "Submitting Picard QualityScoreDistribution #{sample_name} Jobs"
+      script_name = generate_script
+      ::Cagnut::JobManage.submit script_name, @job_name, queuing_options(previous_job_id)
+      @job_name
+    end
+
+    def queuing_options previous_job_id = nil
+      {
+        previous_job_id: previous_job_id,
+        adjust_memory: ['h_vmem=5G'],
+        tools: ['picard', 'quailty_score_distribution']
+      }
+    end
+
+    def quailty_score_distribution_options
+      array = quailty_score_distribution_params['params'].dup
+      array << "INPUT=#{@input}"
+      array << "OUTPUT=#{@output}"
+      array << "CHART_OUTPUT=#{@chart_output}"
+      array << "TMP_DIR=#{@tmp_dir}"
+      array.uniq
+    end
+
+    def modified_java_array
+      array = quailty_score_distribution_params['java'].dup
+      array << 'QualityScoreDistribution'
+      array.unshift(java_path).uniq
+    end
+
+    def params_combination_hash
+      @params_combination_hash ||= {
+        'java' => modified_java_array,
+        'params' => quailty_score_distribution_options
+      }
+    end
+
+    def generate_script
+      script_name = "#{@order}_picard_meanQScDis"
+      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 $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"
+          #{params_combination_hash['java'].join("\s")} \\
+            #{params_combination_hash['params'].join(" \\\n            ")} \\
+            #{::Cagnut::JobManage.run_local}
+
+          EXITSTATUS=$?
+          if [ ! -s "#{@chart_output}" ]; then 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
+  end
+end

data/lib/cagnut_picard/functions/sort_sam.rb

@@ -0,0 +1,89 @@
+module CagnutPicard
+  class SortSam
+    extend Forwardable
+
+    def_delegators :'Cagnut::Configuration.base', :sample_name, :dodebug,
+                   :jobs_dir, :magic28, :ref_fasta, :prefix_name, :java_path
+    def_delegators :'CagnutPicard.config', :rg_str_picard, :sort_sam_params
+
+    def initialize opts = {}
+      @order = sprintf '%02i', opts[:order]
+      @input = opts[:input].nil? ? "#{opts[:dirs][:input]}/#{sample_name}_mem.sam" : opts[:input]
+      @output = "#{opts[:dirs][:output]}/#{sample_name}_sort.bam"
+      @job_name = "#{prefix_name}_sort_sam_#{sample_name}"
+    end
+
+    def run previous_job_id = nil
+      puts "Submitting sort_sam #{sample_name}"
+      script_name = generate_script
+      ::Cagnut::JobManage.submit script_name, @job_name, queuing_options(previous_job_id)
+      [@job_name, @output]
+    end
+
+    def queuing_options previous_job_id = nil
+      {
+        previous_job_id: previous_job_id,
+        tools: ['picard', 'sort_sam']
+      }
+    end
+
+    def sort_sam_options
+      array = sort_sam_params['params'].dup
+      array << "I=#{@input}"
+      array << "O=#{@output}"
+      array.uniq
+    end
+
+    def modified_java_array
+      array = sort_sam_params['java'].dup
+      array << 'SortSam'
+      array.unshift(java_path).uniq
+    end
+
+    def params_combination_hash
+      @params_combination_hash ||= {
+        'java' => modified_java_array,
+        'params' => sort_sam_options
+      }
+    end
+
+    def generate_script
+      script_name = "#{@order}_picard_sort_sam"
+      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 $(date +%Y%m%d%H%M%S)" >> "#{jobs_dir}/finished_jobs"
+          #{params_combination_hash['java'].join("\s")} \\
+            #{params_combination_hash['params'].join(" \\\n            ")} \\
+            #{::Cagnut::JobManage.run_local}
+
+          EXITSTATUS=$?
+
+          if [ ! -e "#{@output}" ]
+          then
+            echo "Missing output: #{@output}"
+            exit 100
+          fi
+
+          # Check BAM EOF
+          BAM_28=$(tail -c 28 #{@output}|xxd -p)
+          if [ '#{magic28}' != "$BAM_28" ]
+          then
+            echo "Error with BAM EOF" 1>&2
+            exit 100
+          fi
+
+          if [ $EXITSTATUS -ne 0 ];then exit $EXITSTATUS;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
+  end
+end

data/lib/cagnut_picard/util.rb

@@ -0,0 +1,62 @@
+module CagnutPicard
+  class Util
+    attr_accessor :picard, :config
+
+    def initialize config
+      @config = config
+      @picard = CagnutPicard::Base.new
+    end
+
+    def add_or_replace_readgroups dirs, order, previous_job_id, filename
+      job_name, filename = picard.add_or_replace_readgroups dirs, order, previous_job_id, filename
+      [job_name, filename, order+1]
+    end
+
+    def markdup dirs, order=1, previous_job_id=nil, filename=nil
+      job_name, filename = picard.markdup dirs, order, previous_job_id, filename
+      [job_name, filename, order+1]
+    end
+
+    def build_bam_index dirs, order=1, previous_job_id=nil, filename=nil
+      job_name = picard.build_bam_index dirs, order, previous_job_id, filename
+      [job_name, order+1]
+    end
+
+    def picard_qc_metrics dirs, order, previous_job_id, filename
+      order = mean_quality_by_cycle dirs, order, previous_job_id, filename
+      order = quality_score_distribution dirs, order, previous_job_id, filename
+      order = collect_gc_bias_metrics dirs, order, previous_job_id, filename
+      collect_insert_size_metrics dirs, order, previous_job_id, filename
+    end
+
+    def mean_quality_by_cycle dirs, order, previous_job_id, filename
+      picard.mean_quality_by_cycle dirs, order, previous_job_id, filename
+      order+1
+    end
+
+    def quality_score_distribution dirs, order, previous_job_id, filename
+      picard.quality_score_distribution dirs, order, previous_job_id, filename
+      order+1
+    end
+
+    def collect_gc_bias_metrics dirs, order, previous_job_id, filename
+      picard.collect_gc_bias_metrics dirs, order, previous_job_id, filename
+      order+1
+    end
+
+    def collect_insert_size_metrics dirs, order, previous_job_id, filename
+      picard.collect_insert_size_metrics dirs, order, previous_job_id, filename
+      order+1
+    end
+
+    def sort_sam dirs, order=1, previous_job_id, filename
+      job_name, filename = picard.sort_sam dirs, order, previous_job_id, filename
+      [job_name, filename, order+1]
+    end
+
+    def collect_multiple_metrics dirs, order=1, previous_job_id, filename
+      picard.collect_multiple_metrics dirs, order, previous_job_id, filename
+      order+1
+    end
+  end
+end

data/lib/cagnut_picard/version.rb

@@ -0,0 +1,3 @@
+module CagnutPicard
+  VERSION = "0.3.0"
+end

data/lib/cagnut_picard.rb

@@ -0,0 +1,16 @@
+require "cagnut_picard/version"
+
+module CagnutPicard
+  class << self
+    def config
+      @config ||= begin
+        CagnutPicard::Configuration.load(Cagnut::Configuration.config, Cagnut::Configuration.params['picard'])
+        CagnutPicard::Configuration.instance
+      end
+    end
+  end
+end
+
+require 'cagnut_picard/configuration'
+require 'cagnut_picard/base'
+require 'cagnut_picard/util'

metadata

@@ -0,0 +1,128 @@
+--- !ruby/object:Gem::Specification
+name: cagnut_picard
+version: !ruby/object:Gem::Version
+  version: 0.3.0
+platform: ruby
+authors:
+- Shi-Gang Wang
+- Tse-Ching Ho
+autorequire: 
+bindir: exe
+cert_chain: []
+date: 2016-11-01 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: cagnut_core
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.12'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.12'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
+description: Cagnut Picard tools
+email:
+- seanwang@goldenio.com
+- tsechingho@goldenio.com
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- ".rspec"
+- ".ruby-version"
+- ".travis.yml"
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- bin/console
+- bin/setup
+- cagnut_picard.gemspec
+- lib/cagnut_picard.rb
+- lib/cagnut_picard/base.rb
+- lib/cagnut_picard/check_tools.rb
+- lib/cagnut_picard/configuration.rb
+- lib/cagnut_picard/functions/add_or_replace_readgroups.rb
+- lib/cagnut_picard/functions/build_bam_index.rb
+- lib/cagnut_picard/functions/collect_gc_bias_metrics.rb
+- lib/cagnut_picard/functions/collect_insert_size_metrics.rb
+- lib/cagnut_picard/functions/collect_multiple_metrics.rb
+- lib/cagnut_picard/functions/markdup.rb
+- lib/cagnut_picard/functions/mean_quality_by_cycle.rb
+- lib/cagnut_picard/functions/quality_score_distribution.rb
+- lib/cagnut_picard/functions/sort_sam.rb
+- lib/cagnut_picard/util.rb
+- lib/cagnut_picard/version.rb
+homepage: https://github.com/CAGNUT/cagnut_picard
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.5.1
+signing_key: 
+specification_version: 4
+summary: Cagnut Picard tools
+test_files: []