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author kkonganti
date Mon, 05 Jun 2023 18:48:51 -0400
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kkonganti@1 1 # CPIPES (CFSAN PIPELINES)
kkonganti@1 2
kkonganti@1 3 ## The modular pipeline repository at CFSAN, FDA
kkonganti@1 4
kkonganti@1 5 **CPIPES** (CFSAN PIPELINES) is a collection of modular pipelines based on **NEXTFLOW**,
kkonganti@1 6 mostly for bioinformatics data analysis at **CFSAN, FDA.**
kkonganti@1 7
kkonganti@1 8 ---
kkonganti@1 9
kkonganti@1 10 ### **LICENSES**
kkonganti@1 11
kkonganti@1 12 \
kkonganti@1 13  
kkonganti@1 14
kkonganti@1 15 **CPIPES** is licensed under:
kkonganti@1 16
kkonganti@1 17 ```text
kkonganti@1 18 MIT License
kkonganti@1 19
kkonganti@1 20 In the U.S.A. Public Domain; elsewhere Copyright (C) 2022 Center for Food Safety and Nutrition (CFSAN)
kkonganti@1 21
kkonganti@1 22 Permission is hereby granted, free of charge, to any person obtaining a copy
kkonganti@1 23 of this software and associated documentation files (the "Software"), to deal
kkonganti@1 24 in the Software without restriction, including without limitation the rights
kkonganti@1 25 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
kkonganti@1 26 copies of the Software, and to permit persons to whom the Software is
kkonganti@1 27 furnished to do so, subject to the following conditions:
kkonganti@1 28
kkonganti@1 29 The above copyright notice and this permission notice shall be included in all
kkonganti@1 30 copies or substantial portions of the Software.
kkonganti@1 31
kkonganti@1 32 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
kkonganti@1 33 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
kkonganti@1 34 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
kkonganti@1 35 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
kkonganti@1 36 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
kkonganti@1 37 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
kkonganti@1 38 SOFTWARE.
kkonganti@1 39 ```
kkonganti@1 40
kkonganti@1 41 \
kkonganti@1 42  
kkonganti@1 43
kkonganti@1 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@1 45
kkonganti@1 46 ```text
kkonganti@1 47 MIT License
kkonganti@1 48
kkonganti@1 49 Copyright (c) Philip Ewels
kkonganti@1 50 Copyright (c) Phil Ewels, Rickard Hammarén
kkonganti@1 51
kkonganti@1 52 Permission is hereby granted, free of charge, to any person obtaining a copy
kkonganti@1 53 of this software and associated documentation files (the "Software"), to deal
kkonganti@1 54 in the Software without restriction, including without limitation the rights
kkonganti@1 55 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
kkonganti@1 56 copies of the Software, and to permit persons to whom the Software is
kkonganti@1 57 furnished to do so, subject to the following conditions:
kkonganti@1 58
kkonganti@1 59 The above copyright notice and this permission notice shall be included in all
kkonganti@1 60 copies or substantial portions of the Software.
kkonganti@1 61
kkonganti@1 62 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
kkonganti@1 63 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
kkonganti@1 64 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
kkonganti@1 65 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
kkonganti@1 66 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
kkonganti@1 67 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
kkonganti@1 68 SOFTWARE.
kkonganti@1 69 ```
kkonganti@1 70
kkonganti@1 71 \
kkonganti@1 72  
kkonganti@1 73
kkonganti@1 74 The **MultiQC** report, in addition uses [DataTables](https://datatables.net), which is licensed under:
kkonganti@1 75
kkonganti@1 76 ```text
kkonganti@1 77 MIT License
kkonganti@1 78
kkonganti@1 79 Copyright (C) 2008-2022, SpryMedia Ltd.
kkonganti@1 80
kkonganti@1 81 Permission is hereby granted, free of charge, to any person obtaining a copy
kkonganti@1 82 of this software and associated documentation files (the "Software"), to deal
kkonganti@1 83 in the Software without restriction, including without limitation the rights
kkonganti@1 84 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
kkonganti@1 85 copies of the Software, and to permit persons to whom the Software is
kkonganti@1 86 furnished to do so, subject to the following conditions:
kkonganti@1 87
kkonganti@1 88 The above copyright notice and this permission notice shall be included in all
kkonganti@1 89 copies or substantial portions of the Software.
kkonganti@1 90
kkonganti@1 91 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
kkonganti@1 92 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
kkonganti@1 93 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
kkonganti@1 94 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
kkonganti@1 95 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
kkonganti@1 96 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
kkonganti@1 97 SOFTWARE.
kkonganti@1 98 ```
kkonganti@1 99
kkonganti@1 100 \
kkonganti@1 101  
kkonganti@1 102
kkonganti@1 103 The **NCBI datasets** is licensed under Public Domain.
kkonganti@1 104
kkonganti@1 105 ```text
kkonganti@1 106 # Public Domain notice
kkonganti@1 107
kkonganti@1 108 National Center for Biotechnology Information
kkonganti@1 109
kkonganti@1 110 This software is a "United States Government Work" under the terms of the
kkonganti@1 111 United States Copyright Act. It was written as part of the authors'
kkonganti@1 112 official duties as United States Government employees and thus cannot
kkonganti@1 113 be copyrighted. This software is freely available to the public for
kkonganti@1 114 use. The National Library of Medicine and the U.S. Government have not
kkonganti@1 115 placed any restriction on its use or reproduction.
kkonganti@1 116
kkonganti@1 117 Although all reasonable efforts have been taken to ensure the accuracy
kkonganti@1 118 and reliability of the software and data, the NLM and the U.S.
kkonganti@1 119 Government do not and cannot warrant the performance or results that
kkonganti@1 120 may be obtained by using this software or data. The NLM and the U.S.
kkonganti@1 121 Government disclaim all warranties, express or implied, including
kkonganti@1 122 warranties of performance, merchantability or fitness for any
kkonganti@1 123 particular purpose.
kkonganti@1 124
kkonganti@1 125 Please cite NCBI in any work or product based on this material.
kkonganti@1 126 ```