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author kkonganti
date Mon, 31 Mar 2025 14:50:40 -0400
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kkonganti@0 1 # CPIPES (CFSAN PIPELINES)
kkonganti@0 2
kkonganti@0 3 ## The modular pipeline repository at CFSAN, FDA
kkonganti@0 4
kkonganti@0 5 **CPIPES** (CFSAN PIPELINES) is a collection of modular pipelines based on **NEXTFLOW**,
kkonganti@0 6 mostly for bioinformatics data analysis at **CFSAN, FDA.**
kkonganti@0 7
kkonganti@0 8 ---
kkonganti@0 9
kkonganti@0 10 ### **LICENSES**
kkonganti@0 11
kkonganti@0 12 \
kkonganti@0 13  
kkonganti@0 14
kkonganti@0 15 **CPIPES** is licensed under:
kkonganti@0 16
kkonganti@0 17 ```text
kkonganti@0 18 MIT License
kkonganti@0 19
kkonganti@0 20 In the U.S.A. Public Domain; elsewhere Copyright (c) 2022 U.S. Food and Drug Administration
kkonganti@0 21
kkonganti@0 22 Permission is hereby granted, free of charge, to any person obtaining a copy
kkonganti@0 23 of this software and associated documentation files (the "Software"), to deal
kkonganti@0 24 in the Software without restriction, including without limitation the rights
kkonganti@0 25 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
kkonganti@0 26 copies of the Software, and to permit persons to whom the Software is
kkonganti@0 27 furnished to do so, subject to the following conditions:
kkonganti@0 28
kkonganti@0 29 The above copyright notice and this permission notice shall be included in all
kkonganti@0 30 copies or substantial portions of the Software.
kkonganti@0 31
kkonganti@0 32 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
kkonganti@0 33 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
kkonganti@0 34 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
kkonganti@0 35 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
kkonganti@0 36 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
kkonganti@0 37 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
kkonganti@0 38 SOFTWARE.
kkonganti@0 39 ```
kkonganti@0 40
kkonganti@0 41 \
kkonganti@0 42  
kkonganti@0 43
kkonganti@0 44 Portions of **CPIPES** are built on modified versions of many tools, scripts and libraries from [nf-core/modules](https://github.com/nf-core/modules) and [nf-core/rnaseq](https://github.com/nf-core/rna-seq) which are originally licensed under:
kkonganti@0 45
kkonganti@0 46 ```text
kkonganti@0 47 MIT License
kkonganti@0 48
kkonganti@0 49 Copyright (c) Philip Ewels
kkonganti@0 50 Copyright (c) Phil Ewels, Rickard Hammarén
kkonganti@0 51
kkonganti@0 52 Permission is hereby granted, free of charge, to any person obtaining a copy
kkonganti@0 53 of this software and associated documentation files (the "Software"), to deal
kkonganti@0 54 in the Software without restriction, including without limitation the rights
kkonganti@0 55 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
kkonganti@0 56 copies of the Software, and to permit persons to whom the Software is
kkonganti@0 57 furnished to do so, subject to the following conditions:
kkonganti@0 58
kkonganti@0 59 The above copyright notice and this permission notice shall be included in all
kkonganti@0 60 copies or substantial portions of the Software.
kkonganti@0 61
kkonganti@0 62 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
kkonganti@0 63 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
kkonganti@0 64 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
kkonganti@0 65 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
kkonganti@0 66 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
kkonganti@0 67 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
kkonganti@0 68 SOFTWARE.
kkonganti@0 69 ```
kkonganti@0 70
kkonganti@0 71 \
kkonganti@0 72  
kkonganti@0 73
kkonganti@0 74 The **MultiQC** report, in addition uses [DataTables](https://datatables.net), which is licensed under:
kkonganti@0 75
kkonganti@0 76 ```text
kkonganti@0 77 MIT License
kkonganti@0 78
kkonganti@0 79 Copyright (C) 2008-2022, SpryMedia Ltd.
kkonganti@0 80
kkonganti@0 81 Permission is hereby granted, free of charge, to any person obtaining a copy
kkonganti@0 82 of this software and associated documentation files (the "Software"), to deal
kkonganti@0 83 in the Software without restriction, including without limitation the rights
kkonganti@0 84 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
kkonganti@0 85 copies of the Software, and to permit persons to whom the Software is
kkonganti@0 86 furnished to do so, subject to the following conditions:
kkonganti@0 87
kkonganti@0 88 The above copyright notice and this permission notice shall be included in all
kkonganti@0 89 copies or substantial portions of the Software.
kkonganti@0 90
kkonganti@0 91 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
kkonganti@0 92 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
kkonganti@0 93 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
kkonganti@0 94 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
kkonganti@0 95 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
kkonganti@0 96 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
kkonganti@0 97 SOFTWARE.
kkonganti@0 98 ```