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date Mon, 15 Jul 2024 12:01:00 -0400
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kkonganti@17 1 # CPIPES (CFSAN PIPELINES)
kkonganti@17 2
kkonganti@17 3 ## The modular pipeline repository at CFSAN, FDA
kkonganti@17 4
kkonganti@17 5 **CPIPES** (CFSAN PIPELINES) is a collection of modular pipelines based on **NEXTFLOW**,
kkonganti@17 6 mostly for bioinformatics data analysis at **CFSAN, FDA.**
kkonganti@17 7
kkonganti@17 8 ---
kkonganti@17 9
kkonganti@17 10 ### **LICENSES**
kkonganti@17 11
kkonganti@17 12 \
kkonganti@17 13  
kkonganti@17 14
kkonganti@17 15 **CPIPES** is licensed under:
kkonganti@17 16
kkonganti@17 17 ```text
kkonganti@17 18 MIT License
kkonganti@17 19
kkonganti@17 20 In the U.S.A. Public Domain; elsewhere Copyright (C) 2022 Center for Food Safety and Nutrition (CFSAN)
kkonganti@17 21
kkonganti@17 22 Permission is hereby granted, free of charge, to any person obtaining a copy
kkonganti@17 23 of this software and associated documentation files (the "Software"), to deal
kkonganti@17 24 in the Software without restriction, including without limitation the rights
kkonganti@17 25 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
kkonganti@17 26 copies of the Software, and to permit persons to whom the Software is
kkonganti@17 27 furnished to do so, subject to the following conditions:
kkonganti@17 28
kkonganti@17 29 The above copyright notice and this permission notice shall be included in all
kkonganti@17 30 copies or substantial portions of the Software.
kkonganti@17 31
kkonganti@17 32 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
kkonganti@17 33 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
kkonganti@17 34 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
kkonganti@17 35 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
kkonganti@17 36 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
kkonganti@17 37 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
kkonganti@17 38 SOFTWARE.
kkonganti@17 39 ```
kkonganti@17 40
kkonganti@17 41 \
kkonganti@17 42  
kkonganti@17 43
kkonganti@17 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:
kkonganti@17 45
kkonganti@17 46 ```text
kkonganti@17 47 MIT License
kkonganti@17 48
kkonganti@17 49 Copyright (c) Philip Ewels
kkonganti@17 50 Copyright (c) Phil Ewels, Rickard Hammarén
kkonganti@17 51
kkonganti@17 52 Permission is hereby granted, free of charge, to any person obtaining a copy
kkonganti@17 53 of this software and associated documentation files (the "Software"), to deal
kkonganti@17 54 in the Software without restriction, including without limitation the rights
kkonganti@17 55 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
kkonganti@17 56 copies of the Software, and to permit persons to whom the Software is
kkonganti@17 57 furnished to do so, subject to the following conditions:
kkonganti@17 58
kkonganti@17 59 The above copyright notice and this permission notice shall be included in all
kkonganti@17 60 copies or substantial portions of the Software.
kkonganti@17 61
kkonganti@17 62 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
kkonganti@17 63 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
kkonganti@17 64 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
kkonganti@17 65 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
kkonganti@17 66 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
kkonganti@17 67 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
kkonganti@17 68 SOFTWARE.
kkonganti@17 69 ```
kkonganti@17 70
kkonganti@17 71 \
kkonganti@17 72  
kkonganti@17 73
kkonganti@17 74 The **MultiQC** report, in addition uses [DataTables](https://datatables.net), which is licensed under:
kkonganti@17 75
kkonganti@17 76 ```text
kkonganti@17 77 MIT License
kkonganti@17 78
kkonganti@17 79 Copyright (C) 2008-2022, SpryMedia Ltd.
kkonganti@17 80
kkonganti@17 81 Permission is hereby granted, free of charge, to any person obtaining a copy
kkonganti@17 82 of this software and associated documentation files (the "Software"), to deal
kkonganti@17 83 in the Software without restriction, including without limitation the rights
kkonganti@17 84 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
kkonganti@17 85 copies of the Software, and to permit persons to whom the Software is
kkonganti@17 86 furnished to do so, subject to the following conditions:
kkonganti@17 87
kkonganti@17 88 The above copyright notice and this permission notice shall be included in all
kkonganti@17 89 copies or substantial portions of the Software.
kkonganti@17 90
kkonganti@17 91 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
kkonganti@17 92 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
kkonganti@17 93 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
kkonganti@17 94 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
kkonganti@17 95 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
kkonganti@17 96 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
kkonganti@17 97 SOFTWARE.
kkonganti@17 98 ```
kkonganti@17 99
kkonganti@17 100 \
kkonganti@17 101  
kkonganti@17 102
kkonganti@17 103 The **NCBI datasets** is licensed under Public Domain.
kkonganti@17 104
kkonganti@17 105 ```text
kkonganti@17 106 # Public Domain notice
kkonganti@17 107
kkonganti@17 108 National Center for Biotechnology Information
kkonganti@17 109
kkonganti@17 110 This software is a "United States Government Work" under the terms of the
kkonganti@17 111 United States Copyright Act. It was written as part of the authors'
kkonganti@17 112 official duties as United States Government employees and thus cannot
kkonganti@17 113 be copyrighted. This software is freely available to the public for
kkonganti@17 114 use. The National Library of Medicine and the U.S. Government have not
kkonganti@17 115 placed any restriction on its use or reproduction.
kkonganti@17 116
kkonganti@17 117 Although all reasonable efforts have been taken to ensure the accuracy
kkonganti@17 118 and reliability of the software and data, the NLM and the U.S.
kkonganti@17 119 Government do not and cannot warrant the performance or results that
kkonganti@17 120 may be obtained by using this software or data. The NLM and the U.S.
kkonganti@17 121 Government disclaim all warranties, express or implied, including
kkonganti@17 122 warranties of performance, merchantability or fitness for any
kkonganti@17 123 particular purpose.
kkonganti@17 124
kkonganti@17 125 Please cite NCBI in any work or product based on this material.
kkonganti@17 126 ```