cagnut_core 0.3.2 → 0.3.3
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- checksums.yaml +4 -4
- data/exe/{stat → stat_lsf_output} +0 -0
- data/lib/cagnut/configuration/checks/datasets.rb +15 -5
- data/lib/cagnut/version.rb +1 -1
- metadata +4 -4
checksums.yaml
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
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---
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|
2
2
|
SHA1:
|
|
3
|
-
metadata.gz:
|
|
4
|
-
data.tar.gz:
|
|
3
|
+
metadata.gz: a6516527142754d04d34191b4358b7a70a9db61d
|
|
4
|
+
data.tar.gz: 3ac9bbf7c0b568d4058fd40027e924d26d773c4f
|
|
5
5
|
SHA512:
|
|
6
|
-
metadata.gz:
|
|
7
|
-
data.tar.gz:
|
|
6
|
+
metadata.gz: 2cac794d277b5b6075ca1df748c82c81ccd0a4c1396e7c30be2274f549af49cb79ce61a39f816ba2a36ef994cda25d693502fd8e4f2b050e550a72762d65a4ad
|
|
7
|
+
data.tar.gz: 7d8ffb98f78fd66f8d14ef5697e6c0d2683157160396a27962694e4bf619d5832e19509af0efa50a123287d6166c62028ff798e0d8cf89ab0000b058f4f513ed
|
|
File without changes
|
|
@@ -74,8 +74,10 @@ module Cagnut
|
|
|
74
74
|
def ln_seq_txt_file sample, qseq_dir
|
|
75
75
|
files =
|
|
76
76
|
Dir.glob("#{sample['path']}/*_sequence.txt*") + Dir.glob("#{sample['path']}/*_qseq.txt*")
|
|
77
|
-
files
|
|
78
|
-
|
|
77
|
+
check_file_size files
|
|
78
|
+
files.each do |file|
|
|
79
|
+
next unless file.match sample['name']
|
|
80
|
+
`ln -s #{file} #{qseq_dir} 2>/dev/null`
|
|
79
81
|
end
|
|
80
82
|
end
|
|
81
83
|
|
|
@@ -86,19 +88,27 @@ module Cagnut
|
|
|
86
88
|
end
|
|
87
89
|
|
|
88
90
|
def ln_fastq_file sample, flist, fastq_dir
|
|
91
|
+
check_file_size flist
|
|
89
92
|
if %w(ONEFASTQ ONEFASTQSE).include? @config['info']['data_type']
|
|
90
93
|
files_to_much? flist
|
|
91
94
|
file_type = link_name flist, sample['name']
|
|
92
95
|
seq_file = "#{fastq_dir}/#{file_type}"
|
|
93
96
|
`ln -s #{flist[0]} #{seq_file} 2>/dev/null` if flist[0].match sample['name']
|
|
94
97
|
else
|
|
95
|
-
flist.each do |
|
|
96
|
-
next unless
|
|
97
|
-
`ln -s #{
|
|
98
|
+
flist.each do |file|
|
|
99
|
+
next unless file.match sample['name']
|
|
100
|
+
`ln -s #{file} #{fastq_dir} 2>/dev/null`
|
|
98
101
|
end
|
|
99
102
|
end
|
|
100
103
|
end
|
|
101
104
|
|
|
105
|
+
def check_file_size flist, previous_size=0
|
|
106
|
+
flist.each do |file|
|
|
107
|
+
file_size = File.size(file)
|
|
108
|
+
abort "#{file} is empty." unless file_size > 0
|
|
109
|
+
end
|
|
110
|
+
end
|
|
111
|
+
|
|
102
112
|
def link_name flist, sample_name
|
|
103
113
|
if flist[0].match '.gz'
|
|
104
114
|
"#{sample_name}_sequence.txt.gz"
|
data/lib/cagnut/version.rb
CHANGED
metadata
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
|
2
2
|
name: cagnut_core
|
|
3
3
|
version: !ruby/object:Gem::Version
|
|
4
|
-
version: 0.3.
|
|
4
|
+
version: 0.3.3
|
|
5
5
|
platform: ruby
|
|
6
6
|
authors:
|
|
7
7
|
- Shi-Gang Wang
|
|
@@ -9,7 +9,7 @@ authors:
|
|
|
9
9
|
autorequire:
|
|
10
10
|
bindir: exe
|
|
11
11
|
cert_chain: []
|
|
12
|
-
date: 2016-
|
|
12
|
+
date: 2016-12-12 00:00:00.000000000 Z
|
|
13
13
|
dependencies:
|
|
14
14
|
- !ruby/object:Gem::Dependency
|
|
15
15
|
name: activesupport
|
|
@@ -101,7 +101,7 @@ email:
|
|
|
101
101
|
- tsechingho@goldenio.com
|
|
102
102
|
executables:
|
|
103
103
|
- cagnut
|
|
104
|
-
-
|
|
104
|
+
- stat_lsf_output
|
|
105
105
|
extensions: []
|
|
106
106
|
extra_rdoc_files: []
|
|
107
107
|
files:
|
|
@@ -117,7 +117,7 @@ files:
|
|
|
117
117
|
- bin/setup
|
|
118
118
|
- cagnut_core.gemspec
|
|
119
119
|
- exe/cagnut
|
|
120
|
-
- exe/
|
|
120
|
+
- exe/stat_lsf_output
|
|
121
121
|
- lib/cagnut.rb
|
|
122
122
|
- lib/cagnut/cli/new_project.rb
|
|
123
123
|
- lib/cagnut/cli/pipeline.rb
|