kkonganti@92: # CPIPES (CFSAN PIPELINES)
kkonganti@92: 
kkonganti@92: ## The modular pipeline repository at CFSAN, FDA
kkonganti@92: 
kkonganti@92: **CPIPES** (CFSAN PIPELINES) is a collection of modular pipelines based on **NEXTFLOW**,
kkonganti@92: mostly for bioinformatics data analysis at **CFSAN, FDA.**
kkonganti@92: 
kkonganti@92: ---
kkonganti@92: 
kkonganti@92: ### **LICENSES**
kkonganti@92: 
kkonganti@92: \
kkonganti@92:  
kkonganti@92: 
kkonganti@92: **CPIPES** is licensed under:
kkonganti@92: 
kkonganti@92: ```text
kkonganti@92: MIT License
kkonganti@92: 
kkonganti@92: In the U.S.A. Public Domain; elsewhere Copyright (c) 2022 U.S. Food and Drug Administration
kkonganti@92: 
kkonganti@92: Permission is hereby granted, free of charge, to any person obtaining a copy
kkonganti@92: of this software and associated documentation files (the "Software"), to deal
kkonganti@92: in the Software without restriction, including without limitation the rights
kkonganti@92: to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
kkonganti@92: copies of the Software, and to permit persons to whom the Software is
kkonganti@92: furnished to do so, subject to the following conditions:
kkonganti@92: 
kkonganti@92: The above copyright notice and this permission notice shall be included in all
kkonganti@92: copies or substantial portions of the Software.
kkonganti@92: 
kkonganti@92: THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
kkonganti@92: IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
kkonganti@92: FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
kkonganti@92: AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
kkonganti@92: LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
kkonganti@92: OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
kkonganti@92: SOFTWARE.
kkonganti@92: ```
kkonganti@92: 
kkonganti@92: \
kkonganti@92:  
kkonganti@92: 
kkonganti@92: 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@92: 
kkonganti@92: ```text
kkonganti@92: MIT License
kkonganti@92: 
kkonganti@92: Copyright (c) Philip Ewels
kkonganti@92: Copyright (c) Phil Ewels, Rickard Hammarén
kkonganti@92: 
kkonganti@92: Permission is hereby granted, free of charge, to any person obtaining a copy
kkonganti@92: of this software and associated documentation files (the "Software"), to deal
kkonganti@92: in the Software without restriction, including without limitation the rights
kkonganti@92: to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
kkonganti@92: copies of the Software, and to permit persons to whom the Software is
kkonganti@92: furnished to do so, subject to the following conditions:
kkonganti@92: 
kkonganti@92: The above copyright notice and this permission notice shall be included in all
kkonganti@92: copies or substantial portions of the Software.
kkonganti@92: 
kkonganti@92: THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
kkonganti@92: IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
kkonganti@92: FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
kkonganti@92: AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
kkonganti@92: LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
kkonganti@92: OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
kkonganti@92: SOFTWARE.
kkonganti@92: ```
kkonganti@92: 
kkonganti@92: \
kkonganti@92:  
kkonganti@92: 
kkonganti@92: The **MultiQC** report, in addition uses [DataTables](https://datatables.net), which is licensed under:
kkonganti@92: 
kkonganti@92: ```text
kkonganti@92: MIT License
kkonganti@92: 
kkonganti@92: Copyright (C) 2008-2022, SpryMedia Ltd.
kkonganti@92: 
kkonganti@92: Permission is hereby granted, free of charge, to any person obtaining a copy
kkonganti@92: of this software and associated documentation files (the "Software"), to deal
kkonganti@92: in the Software without restriction, including without limitation the rights
kkonganti@92: to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
kkonganti@92: copies of the Software, and to permit persons to whom the Software is
kkonganti@92: furnished to do so, subject to the following conditions:
kkonganti@92: 
kkonganti@92: The above copyright notice and this permission notice shall be included in all
kkonganti@92: copies or substantial portions of the Software.
kkonganti@92: 
kkonganti@92: THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
kkonganti@92: IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
kkonganti@92: FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
kkonganti@92: AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
kkonganti@92: LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
kkonganti@92: OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
kkonganti@92: SOFTWARE.
kkonganti@92: ```