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1 # CPIPES (CFSAN PIPELINES)
2
3 ## The modular pipeline repository at CFSAN, FDA
4
5 **CPIPES** (CFSAN PIPELINES) is a collection of modular pipelines based on **NEXTFLOW**,
6 mostly for bioinformatics data analysis at **CFSAN, FDA.**
7
8 ---
9
10 ### **LICENSES**
11
12 \
13  
14
15 **CPIPES** is licensed under:
16
17 ```text
18 MIT License
19
20 In the U.S.A. Public Domain; elsewhere Copyright (C) 2022 Center for Food Safety and Nutrition (CFSAN)
21
22 Permission is hereby granted, free of charge, to any person obtaining a copy
23 of this software and associated documentation files (the "Software"), to deal
24 in the Software without restriction, including without limitation the rights
25 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
26 copies of the Software, and to permit persons to whom the Software is
27 furnished to do so, subject to the following conditions:
28
29 The above copyright notice and this permission notice shall be included in all
30 copies or substantial portions of the Software.
31
32 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
33 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
34 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
35 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
36 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
37 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
38 SOFTWARE.
39 ```
40
41 \
42  
43
44 Major portions of **CPIPES** are built on modified versions of many modules, scripts and libraries from [nf-core/modules](https://github.com/nf-core/modules) and [nf-core/rnaseq](https://github.com/nf-core/rnaseq) which are originally licensed under:
45
46 ```text
47 MIT License
48
49 Copyright (c) Philip Ewels
50 Copyright (c) Phil Ewels, Rickard Hammarén
51
52 Permission is hereby granted, free of charge, to any person obtaining a copy
53 of this software and associated documentation files (the "Software"), to deal
54 in the Software without restriction, including without limitation the rights
55 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
56 copies of the Software, and to permit persons to whom the Software is
57 furnished to do so, subject to the following conditions:
58
59 The above copyright notice and this permission notice shall be included in all
60 copies or substantial portions of the Software.
61
62 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
63 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
64 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
65 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
66 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
67 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
68 SOFTWARE.
69 ```
70
71 \
72  
73
74 The **MultiQC** report, in addition uses [DataTables](https://datatables.net), which is licensed under:
75
76 ```text
77 MIT License
78
79 Copyright (C) 2008-2022, SpryMedia Ltd.
80
81 Permission is hereby granted, free of charge, to any person obtaining a copy
82 of this software and associated documentation files (the "Software"), to deal
83 in the Software without restriction, including without limitation the rights
84 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
85 copies of the Software, and to permit persons to whom the Software is
86 furnished to do so, subject to the following conditions:
87
88 The above copyright notice and this permission notice shall be included in all
89 copies or substantial portions of the Software.
90
91 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
92 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
93 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
94 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
95 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
96 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
97 SOFTWARE.
98 ```
99
100 \
101  
102
103 The **NCBI datasets** is licensed under Public Domain.
104
105 ```text
106 # Public Domain notice
107
108 National Center for Biotechnology Information
109
110 This software is a "United States Government Work" under the terms of the
111 United States Copyright Act. It was written as part of the authors'
112 official duties as United States Government employees and thus cannot
113 be copyrighted. This software is freely available to the public for
114 use. The National Library of Medicine and the U.S. Government have not
115 placed any restriction on its use or reproduction.
116
117 Although all reasonable efforts have been taken to ensure the accuracy
118 and reliability of the software and data, the NLM and the U.S.
119 Government do not and cannot warrant the performance or results that
120 may be obtained by using this software or data. The NLM and the U.S.
121 Government disclaim all warranties, express or implied, including
122 warranties of performance, merchantability or fitness for any
123 particular purpose.
124
125 Please cite NCBI in any work or product based on this material.
126 ```