cagnut_pipeline_draw 0.3.1
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +7 -0
- data/.gitignore +9 -0
- data/.rspec +2 -0
- data/.ruby-version +1 -0
- data/.travis.yml +5 -0
- data/Gemfile +4 -0
- data/LICENSE.txt +21 -0
- data/README.md +35 -0
- data/Rakefile +6 -0
- data/bin/console +14 -0
- data/bin/setup +8 -0
- data/cagnut_pipeline_draw.gemspec +33 -0
- data/lib/cagnut_pipeline_draw.rb +30 -0
- data/lib/cagnut_pipeline_draw/cli/new_project/draw.rb +32 -0
- data/lib/cagnut_pipeline_draw/cli/pipeline/draw.rb +38 -0
- data/lib/cagnut_pipeline_draw/configuration.rb +39 -0
- data/lib/cagnut_pipeline_draw/pipeline/alignment.rb +80 -0
- data/lib/cagnut_pipeline_draw/pipeline/recalibration.rb +65 -0
- data/lib/cagnut_pipeline_draw/pipeline/variant_call.rb +54 -0
- data/lib/cagnut_pipeline_draw/version.rb +3 -0
- data/templates/draw_tools.yml +142 -0
- metadata +206 -0
checksums.yaml
ADDED
@@ -0,0 +1,7 @@
|
|
1
|
+
---
|
2
|
+
SHA1:
|
3
|
+
metadata.gz: d2df12ac2d6e44d27a196d4a2b9121e6d9e069b7
|
4
|
+
data.tar.gz: 5159cf7f096c9624885feb71fd47abf6d19372b9
|
5
|
+
SHA512:
|
6
|
+
metadata.gz: 13f1034a156216120976e3a2d2101e54f5cc5e1225997bdcfc136e975469c1dc1acb839b683aafbe1ec7742b9121ef7141ca498a4df8616468ef3af3b57c36c1
|
7
|
+
data.tar.gz: ec2622bd11631dc9fcb0592a851406134daf6597b4de95b9806c50b4b761d47e0b7c396927a8af604d91cdfc10b54e84a48c2acad3b580d1dc1c6075a3ec3209
|
data/.gitignore
ADDED
data/.rspec
ADDED
data/.ruby-version
ADDED
@@ -0,0 +1 @@
|
|
1
|
+
ruby-2.3.1
|
data/.travis.yml
ADDED
data/Gemfile
ADDED
data/LICENSE.txt
ADDED
@@ -0,0 +1,21 @@
|
|
1
|
+
The MIT License (MIT)
|
2
|
+
|
3
|
+
Copyright (c) 2016 Goldenio Technology
|
4
|
+
|
5
|
+
Permission is hereby granted, free of charge, to any person obtaining a copy
|
6
|
+
of this software and associated documentation files (the "Software"), to deal
|
7
|
+
in the Software without restriction, including without limitation the rights
|
8
|
+
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
|
9
|
+
copies of the Software, and to permit persons to whom the Software is
|
10
|
+
furnished to do so, subject to the following conditions:
|
11
|
+
|
12
|
+
The above copyright notice and this permission notice shall be included in
|
13
|
+
all copies or substantial portions of the Software.
|
14
|
+
|
15
|
+
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
|
16
|
+
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
|
17
|
+
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
|
18
|
+
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
|
19
|
+
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
|
20
|
+
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
|
21
|
+
THE SOFTWARE.
|
data/README.md
ADDED
@@ -0,0 +1,35 @@
|
|
1
|
+
# CagnutPipelineDraw
|
2
|
+
|
3
|
+
## Installation
|
4
|
+
|
5
|
+
Add this line to your application's Gemfile:
|
6
|
+
|
7
|
+
```ruby
|
8
|
+
gem 'cagnut_pipeline_draw'
|
9
|
+
```
|
10
|
+
|
11
|
+
And then execute:
|
12
|
+
|
13
|
+
$ bundle
|
14
|
+
|
15
|
+
Or install it yourself as:
|
16
|
+
|
17
|
+
$ gem install cagnut_pipeline_draw
|
18
|
+
|
19
|
+
## Usage
|
20
|
+
|
21
|
+
## Development
|
22
|
+
|
23
|
+
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.
|
24
|
+
|
25
|
+
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).
|
26
|
+
|
27
|
+
## Contributing
|
28
|
+
|
29
|
+
Bug reports and pull requests are welcome on GitHub at https://github.com/[USERNAME]/cagnut_pipeline_draw.
|
30
|
+
|
31
|
+
|
32
|
+
## License
|
33
|
+
|
34
|
+
The gem is available as open source under the terms of the [MIT License](http://opensource.org/licenses/MIT).
|
35
|
+
|
data/Rakefile
ADDED
data/bin/console
ADDED
@@ -0,0 +1,14 @@
|
|
1
|
+
#!/usr/bin/env ruby
|
2
|
+
|
3
|
+
require "bundler/setup"
|
4
|
+
require "cagnut_pipeline_draw"
|
5
|
+
|
6
|
+
# You can add fixtures and/or initialization code here to make experimenting
|
7
|
+
# with your gem easier. You can also use a different console, if you like.
|
8
|
+
|
9
|
+
# (If you use this, don't forget to add pry to your Gemfile!)
|
10
|
+
# require "pry"
|
11
|
+
# Pry.start
|
12
|
+
|
13
|
+
require "irb"
|
14
|
+
IRB.start
|
data/bin/setup
ADDED
@@ -0,0 +1,33 @@
|
|
1
|
+
# coding: utf-8
|
2
|
+
lib = File.expand_path('../lib', __FILE__)
|
3
|
+
$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
|
4
|
+
require 'cagnut_pipeline_draw/version'
|
5
|
+
|
6
|
+
Gem::Specification.new do |spec|
|
7
|
+
spec.name = "cagnut_pipeline_draw"
|
8
|
+
spec.version = CagnutPipelineDraw::VERSION
|
9
|
+
spec.authors = ['Shi-Gang Wang', 'Tse-Ching Ho']
|
10
|
+
spec.email = ['seanwang@goldenio.com', 'tsechingho@goldenio.com']
|
11
|
+
|
12
|
+
spec.summary = %q{Cagnut Draw Pipeline}
|
13
|
+
spec.description = %q{Cagnut Draw Pipeline}
|
14
|
+
spec.homepage = "https://github.com/CAGNUT/cagnut_pipeline_draw"
|
15
|
+
spec.license = "MIT"
|
16
|
+
|
17
|
+
spec.files = `git ls-files -z`.split("\x0").reject { |f| f.match(%r{^(test|spec|features)/}) }
|
18
|
+
spec.bindir = "exe"
|
19
|
+
spec.executables = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
|
20
|
+
spec.require_paths = ["lib"]
|
21
|
+
|
22
|
+
spec.add_dependency 'cagnut_core'
|
23
|
+
spec.add_dependency 'cagnut_bwa'
|
24
|
+
spec.add_dependency 'cagnut_gatk'
|
25
|
+
spec.add_dependency 'cagnut_samtools'
|
26
|
+
spec.add_dependency 'cagnut_picard'
|
27
|
+
spec.add_dependency 'cagnut_snpeff'
|
28
|
+
spec.add_dependency 'cagnut_toolbox'
|
29
|
+
|
30
|
+
spec.add_development_dependency "bundler", "~> 1.12"
|
31
|
+
spec.add_development_dependency "rake", "~> 10.0"
|
32
|
+
spec.add_development_dependency "rspec", "~> 3.0"
|
33
|
+
end
|
@@ -0,0 +1,30 @@
|
|
1
|
+
require "cagnut_pipeline_draw/version"
|
2
|
+
require 'cagnut_bwa'
|
3
|
+
require 'cagnut_gatk'
|
4
|
+
require 'cagnut_picard'
|
5
|
+
require 'cagnut_samtools'
|
6
|
+
require 'cagnut_snpeff'
|
7
|
+
require 'cagnut_toolbox'
|
8
|
+
|
9
|
+
module CagnutPipelineDraw
|
10
|
+
class << self
|
11
|
+
def pipeline_names
|
12
|
+
%W(draw1 draw2 draw3 draw)
|
13
|
+
end
|
14
|
+
|
15
|
+
def config_name
|
16
|
+
'draw'
|
17
|
+
end
|
18
|
+
|
19
|
+
def root
|
20
|
+
::Pathname.new File.expand_path '../..', __FILE__
|
21
|
+
end
|
22
|
+
end
|
23
|
+
end
|
24
|
+
|
25
|
+
require 'cagnut_pipeline_draw/configuration'
|
26
|
+
require 'cagnut_pipeline_draw/cli/new_project/draw'
|
27
|
+
require 'cagnut_pipeline_draw/cli/pipeline/draw'
|
28
|
+
require "cagnut_pipeline_draw/pipeline/alignment"
|
29
|
+
require "cagnut_pipeline_draw/pipeline/recalibration"
|
30
|
+
require "cagnut_pipeline_draw/pipeline/variant_call"
|
@@ -0,0 +1,32 @@
|
|
1
|
+
module Cagnut
|
2
|
+
module Cli
|
3
|
+
module NewProject
|
4
|
+
module Draw
|
5
|
+
|
6
|
+
def actgun_pipeline_draw_root
|
7
|
+
CagnutPipelineDraw.root.join('templates')
|
8
|
+
end
|
9
|
+
|
10
|
+
def copy_draw_tools_config folder
|
11
|
+
draw_tools_yml = File.join(actgun_pipeline_draw_root, 'draw_tools.yml')
|
12
|
+
copy_file "#{draw_tools_yml}", "#{folder}/draw_tools.yml"
|
13
|
+
end
|
14
|
+
|
15
|
+
def draw_pipeline_dependency_gems
|
16
|
+
%W(
|
17
|
+
'cagnut_core'
|
18
|
+
'cagnut_bwa'
|
19
|
+
'cagnut_gatk'
|
20
|
+
'cagnut_samtools'
|
21
|
+
'cagnut_picard'
|
22
|
+
'cagnut_snpeff'
|
23
|
+
'cagnut_toolbox'
|
24
|
+
)
|
25
|
+
end
|
26
|
+
|
27
|
+
end
|
28
|
+
end
|
29
|
+
end
|
30
|
+
end
|
31
|
+
|
32
|
+
Cagnut::NewProject.prepend Cagnut::Cli::NewProject::Draw
|
@@ -0,0 +1,38 @@
|
|
1
|
+
module Cagnut
|
2
|
+
module Cli
|
3
|
+
module Pipeline
|
4
|
+
module Draw
|
5
|
+
|
6
|
+
def pipeline_draw opts = {}
|
7
|
+
opts[:job_name], opts[:filename], order = pipeline_draw1
|
8
|
+
opts[:job_name], opts[:filename], order = pipeline_draw2 opts, order
|
9
|
+
opts[:job_name], opts[:filename], order = pipeline_draw3 opts, order
|
10
|
+
end
|
11
|
+
|
12
|
+
def pipeline_draw1 opts = {}, order=1
|
13
|
+
puts 'Phase 1 - Create BAM alignments'
|
14
|
+
CagnutPipelineDraw::Pipeline::Alignment.new.run order
|
15
|
+
end
|
16
|
+
|
17
|
+
def pipeline_draw2 opts = {}, order=1
|
18
|
+
puts 'Phase 2 - BAM Recalibration'
|
19
|
+
CagnutPipelineDraw::Pipeline::Recalibration.new(opts[:job_name]).run opts[:filename], order
|
20
|
+
end
|
21
|
+
|
22
|
+
def pipeline_draw3 opts = {}, order=1
|
23
|
+
puts 'Phase 3 - VariantCall and Generate Stats'
|
24
|
+
CagnutPipelineDraw::Pipeline::VariantCall.new(opts[:job_name]).run opts[:filename], order
|
25
|
+
end
|
26
|
+
|
27
|
+
def run_filter names
|
28
|
+
return if names.size <= 3 && names.all? { |name| CagnutPipelineDraw.pipeline_names.include? name }
|
29
|
+
super
|
30
|
+
end
|
31
|
+
|
32
|
+
end
|
33
|
+
end
|
34
|
+
end
|
35
|
+
end
|
36
|
+
|
37
|
+
Cagnut::Pipeline::Base.prepend Cagnut::Cli::Pipeline::Draw
|
38
|
+
Cagnut::Pipeline::Base.register CagnutPipelineDraw
|
@@ -0,0 +1,39 @@
|
|
1
|
+
module CagnutPipelineDraw
|
2
|
+
module Configuration
|
3
|
+
|
4
|
+
module Utils
|
5
|
+
class << self
|
6
|
+
def create_output_dirs config, index, dir
|
7
|
+
draw_pipeline_folders.each do |folder_name|
|
8
|
+
FileUtils.mkdir_p "#{dir}/#{folder_name}"
|
9
|
+
config['samples'][index]["#{folder_name}"] = "#{dir}/#{folder_name}"
|
10
|
+
end
|
11
|
+
end
|
12
|
+
|
13
|
+
def draw_pipeline_folders
|
14
|
+
%W(
|
15
|
+
bam
|
16
|
+
csv
|
17
|
+
fastq
|
18
|
+
qseq
|
19
|
+
stat
|
20
|
+
sai
|
21
|
+
sam
|
22
|
+
tmp
|
23
|
+
vcf
|
24
|
+
)
|
25
|
+
end
|
26
|
+
end
|
27
|
+
end
|
28
|
+
|
29
|
+
def make_required_folders config, sample, index, analysis_folder
|
30
|
+
super
|
31
|
+
return unless CagnutPipelineDraw.config_name == config['pipeline_name']
|
32
|
+
CagnutPipelineDraw::Configuration::Utils.create_output_dirs config, index, analysis_folder
|
33
|
+
ln_seq_files_to_folder sample, sample['qseq'], sample['fastq']
|
34
|
+
end
|
35
|
+
|
36
|
+
end
|
37
|
+
end
|
38
|
+
|
39
|
+
Cagnut::Configuration::Checks::Datasets.prepend CagnutPipelineDraw::Configuration
|
@@ -0,0 +1,80 @@
|
|
1
|
+
module CagnutPipelineDraw
|
2
|
+
module Pipeline
|
3
|
+
class Alignment
|
4
|
+
attr_accessor :bwa, :samtools, :picard, :toolbox
|
5
|
+
|
6
|
+
def initialize
|
7
|
+
@config = Cagnut::Configuration.config
|
8
|
+
@bwa = ::CagnutBwa::Util.new @config
|
9
|
+
@samtools = ::CagnutSamtools::Util.new
|
10
|
+
@picard = ::CagnutPicard::Util.new @config
|
11
|
+
@toolbox = ::CagnutToolbox::Util.new @config
|
12
|
+
end
|
13
|
+
|
14
|
+
def run order=1
|
15
|
+
case @config['data_type']
|
16
|
+
when 'BAM'
|
17
|
+
puts 'Merging the following bam files'
|
18
|
+
bam_dir = @config['bam_dir']
|
19
|
+
puts Dir.entries(bam_dir).select { |f| !File.directory? f }
|
20
|
+
@samtools.merge_bam samtools_merge_bam_dirs, order
|
21
|
+
when 'ONEFASTQ', 'ONEFASTQSE'
|
22
|
+
job_name, order = @bwa.aln_one_fastq bwa_aln_dirs, order
|
23
|
+
job_name, filename, order = @bwa.samp_one_fastq bwa_samp_dirs, order, job_name
|
24
|
+
job_name, filename, order = @picard.add_or_replace_readgroups picard_add_read_group_dirs, order, job_name, filename
|
25
|
+
@samtools.mg_bam_soft_link samtools_mg_bam_soft_link_dirs, order, job_name, filename
|
26
|
+
else
|
27
|
+
job_name, filename, order = @toolbox.qseq2fastq toolbox_qseq2fastq_dirs, order
|
28
|
+
job_name, order = @bwa.aln bwa_aln_dirs, order, job_name, filename
|
29
|
+
job_name, filename, order = @bwa.samp bwa_samp_dirs, order, job_name, filename
|
30
|
+
job_name, filename, order = @picard.add_or_replace_readgroups picard_add_read_group_dirs, order, job_name, filename
|
31
|
+
@samtools.merge_bam samtools_merge_bam_dirs, order, job_name, filename
|
32
|
+
end
|
33
|
+
end
|
34
|
+
|
35
|
+
private
|
36
|
+
|
37
|
+
def toolbox_qseq2fastq_dirs
|
38
|
+
{
|
39
|
+
output: @config['sample']['fastq']
|
40
|
+
}
|
41
|
+
end
|
42
|
+
|
43
|
+
def bwa_samp_dirs
|
44
|
+
{
|
45
|
+
input: @config['sample']['sai'],
|
46
|
+
output: @config['sample']['sam']
|
47
|
+
}
|
48
|
+
end
|
49
|
+
|
50
|
+
def bwa_aln_dirs
|
51
|
+
{
|
52
|
+
output: @config['sample']['sai']
|
53
|
+
}
|
54
|
+
end
|
55
|
+
|
56
|
+
def samtools_mg_bam_soft_link_dirs
|
57
|
+
{
|
58
|
+
input: @config['sample']['bam'],
|
59
|
+
output: @config['sample']['bam']
|
60
|
+
}
|
61
|
+
end
|
62
|
+
|
63
|
+
def picard_add_read_group_dirs
|
64
|
+
{
|
65
|
+
input: @config['sample']['sam'],
|
66
|
+
output: @config['sample']['bam'],
|
67
|
+
tmp_dir: @config['sample']['tmp']
|
68
|
+
}
|
69
|
+
end
|
70
|
+
|
71
|
+
def samtools_merge_bam_dirs
|
72
|
+
{
|
73
|
+
input: @config['sample']['sam'],
|
74
|
+
output: @config['sample']['bam']
|
75
|
+
}
|
76
|
+
end
|
77
|
+
|
78
|
+
end
|
79
|
+
end
|
80
|
+
end
|
@@ -0,0 +1,65 @@
|
|
1
|
+
module CagnutPipelineDraw
|
2
|
+
module Pipeline
|
3
|
+
class Recalibration
|
4
|
+
attr_accessor :gatk, :picard, :samtools
|
5
|
+
|
6
|
+
def initialize job_name
|
7
|
+
@job_name = job_name
|
8
|
+
@config = Cagnut::Configuration.config
|
9
|
+
@gatk = ::CagnutGatk::Util.new @config
|
10
|
+
@picard = ::CagnutPicard::Util.new @config
|
11
|
+
@samtools = ::CagnutSamtools::Util.new
|
12
|
+
end
|
13
|
+
|
14
|
+
def run filename = nil, order=1
|
15
|
+
job_name, filename, order = picard.markdup picard_markup_dirs, order, @job_name, filename
|
16
|
+
order = samtools.do_flag_stat samtools_do_flag_stat_dirs, order, job_name, filename
|
17
|
+
order = gatk.count_read gatk_count_read_dirs, order, job_name, filename
|
18
|
+
job_name, filename, order = gatk.recal gatk_recal_dirs, order, job_name, filename
|
19
|
+
order = picard.picard_qc_metrics picard_picard_qc_metrics_dirs, order, job_name, filename
|
20
|
+
[job_name, filename, order]
|
21
|
+
end
|
22
|
+
|
23
|
+
private
|
24
|
+
|
25
|
+
def picard_markup_dirs
|
26
|
+
{
|
27
|
+
input: @config['sample']['bam'],
|
28
|
+
output: @config['sample']['bam'],
|
29
|
+
tmp_dir: @config['sample']['tmp']
|
30
|
+
}
|
31
|
+
end
|
32
|
+
|
33
|
+
def samtools_do_flag_stat_dirs
|
34
|
+
{
|
35
|
+
input: @config['sample']['bam'],
|
36
|
+
output: @config['sample']['stat']
|
37
|
+
}
|
38
|
+
end
|
39
|
+
|
40
|
+
def gatk_count_read_dirs
|
41
|
+
{
|
42
|
+
input: @config['sample']['bam'],
|
43
|
+
output: @config['sample']['stat']
|
44
|
+
}
|
45
|
+
end
|
46
|
+
|
47
|
+
def gatk_recal_dirs
|
48
|
+
{
|
49
|
+
input: @config['sample']['bam'],
|
50
|
+
output: @config['sample']['bam'],
|
51
|
+
contrast: @config['sample']['bam']
|
52
|
+
}
|
53
|
+
end
|
54
|
+
|
55
|
+
def picard_picard_qc_metrics_dirs
|
56
|
+
{
|
57
|
+
input: @config['sample']['bam'],
|
58
|
+
output: @config['sample']['stat'],
|
59
|
+
tmp_dir: @config['sample']['tmp']
|
60
|
+
}
|
61
|
+
end
|
62
|
+
|
63
|
+
end
|
64
|
+
end
|
65
|
+
end
|
@@ -0,0 +1,54 @@
|
|
1
|
+
module CagnutPipelineDraw
|
2
|
+
module Pipeline
|
3
|
+
class VariantCall
|
4
|
+
attr_accessor :gatk, :snp_eff
|
5
|
+
|
6
|
+
def initialize job_name
|
7
|
+
@job_name = job_name
|
8
|
+
@config = Cagnut::Configuration.config
|
9
|
+
@gatk = ::CagnutGatk::Util.new @config
|
10
|
+
@snpeff = ::CagnutSnpeff::Util.new
|
11
|
+
end
|
12
|
+
|
13
|
+
def run filename = nil, order=1
|
14
|
+
order = @gatk.depth_of_coverage gatk_depth_of_coverage_dirs, order, @job_name, filename
|
15
|
+
job_name, filename, order = @gatk.unified_genotyper gatk_unified_genotyper_dirs, order, @job_name, filename
|
16
|
+
job_name, filename, order = @gatk.snpcal gatk_snpcal_dirs, order, job_name, filename
|
17
|
+
job_name, order = @snpeff.snp_annotation snpeff_snp_annotation_dirs, order, job_name, filename
|
18
|
+
# collectSPeekMetrics
|
19
|
+
[job_name, nil, order+1]
|
20
|
+
end
|
21
|
+
|
22
|
+
private
|
23
|
+
|
24
|
+
def gatk_depth_of_coverage_dirs
|
25
|
+
{
|
26
|
+
input: @config['sample']['bam'],
|
27
|
+
output: @config['sample']['stat'],
|
28
|
+
}
|
29
|
+
end
|
30
|
+
|
31
|
+
def gatk_snpcal_dirs
|
32
|
+
{
|
33
|
+
input: @config['sample']['bam'],
|
34
|
+
output: @config['sample']['vcf'],
|
35
|
+
}
|
36
|
+
end
|
37
|
+
|
38
|
+
def gatk_unified_genotyper_dirs
|
39
|
+
{
|
40
|
+
input: @config['sample']['vcf'],
|
41
|
+
output: @config['sample']['vcf'],
|
42
|
+
}
|
43
|
+
end
|
44
|
+
|
45
|
+
def snpeff_snp_annotation_dirs
|
46
|
+
{
|
47
|
+
input: @config['sample']['vcf'],
|
48
|
+
output: @config['sample']['vcf'],
|
49
|
+
}
|
50
|
+
end
|
51
|
+
|
52
|
+
end
|
53
|
+
end
|
54
|
+
end
|
@@ -0,0 +1,142 @@
|
|
1
|
+
bwa:
|
2
|
+
aln:
|
3
|
+
params:
|
4
|
+
- -t 16
|
5
|
+
samp:
|
6
|
+
params:
|
7
|
+
-
|
8
|
+
|
9
|
+
gatk:
|
10
|
+
base_recalibrator:
|
11
|
+
java:
|
12
|
+
- -Xmx4g
|
13
|
+
params:
|
14
|
+
- -l INFO
|
15
|
+
- -nct 16
|
16
|
+
count_reads:
|
17
|
+
java:
|
18
|
+
- -Xmx2g
|
19
|
+
params:
|
20
|
+
- --read_filter MappingQualityUnavailable
|
21
|
+
- --read_filter UnmappedRead
|
22
|
+
- --read_filter DuplicateRead
|
23
|
+
- --read_filter MappingQualityZero
|
24
|
+
depth_of_coverage:
|
25
|
+
java:
|
26
|
+
- -Xmx5g
|
27
|
+
params:
|
28
|
+
- -l INFO
|
29
|
+
- --summaryCoverageThreshold 10
|
30
|
+
- --summaryCoverageThreshold 20
|
31
|
+
indel_realigner:
|
32
|
+
java:
|
33
|
+
- -Xmx5g
|
34
|
+
params:
|
35
|
+
- --maxReadsInMemory 200000
|
36
|
+
print_reads:
|
37
|
+
java:
|
38
|
+
- -Xmx2g
|
39
|
+
params:
|
40
|
+
- -l INFO
|
41
|
+
- -nct 16
|
42
|
+
realigner_target_creator:
|
43
|
+
java:
|
44
|
+
- -Xmx2g
|
45
|
+
params:
|
46
|
+
- -nt 2
|
47
|
+
unified_genotyper:
|
48
|
+
java:
|
49
|
+
- -Xmx4g
|
50
|
+
params:
|
51
|
+
- -nt 6
|
52
|
+
- -mbq 20
|
53
|
+
- -mmq 30
|
54
|
+
- -l INFO
|
55
|
+
- --read_filter MappingQuality
|
56
|
+
- --read_filter DuplicateRead
|
57
|
+
- --genotype_likelihoods_model BOTH
|
58
|
+
variant_eval:
|
59
|
+
java:
|
60
|
+
- -Xmx4g
|
61
|
+
params:
|
62
|
+
- -EV CountVariants
|
63
|
+
variant_filtration:
|
64
|
+
java:
|
65
|
+
- -Xmx4g
|
66
|
+
params:
|
67
|
+
- --clusterWindowSize 10
|
68
|
+
- --filterName "HomopolymerRun"
|
69
|
+
- --filterExpression "HRun>=4"
|
70
|
+
- --filterName "QualByDepth"
|
71
|
+
- --filterExpression "QD<5.0"
|
72
|
+
- --filterName "StrandBias"
|
73
|
+
- --filterExpression "FS>=20.0"
|
74
|
+
- -l INFO
|
75
|
+
|
76
|
+
picard:
|
77
|
+
add_or_replace_readgroups:
|
78
|
+
java:
|
79
|
+
- -Xmx4g
|
80
|
+
params:
|
81
|
+
- VALIDATION_STRINGENCY=SILENT
|
82
|
+
- MAX_RECORDS_IN_RAM=1000000
|
83
|
+
- SORT_ORDER=coordinate
|
84
|
+
- 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: []
|