kkonganti@11: # CPIPES (CFSAN PIPELINES)
kkonganti@11: 
kkonganti@11: ## The modular pipeline repository at CFSAN, FDA
kkonganti@11: 
kkonganti@11: **CPIPES** (CFSAN PIPELINES) is a collection of modular pipelines based on **NEXTFLOW**,
kkonganti@11: mostly for bioinformatics data analysis at **CFSAN, FDA.**
kkonganti@11: 
kkonganti@11: ---
kkonganti@11: 
kkonganti@11: ### **LICENSES**
kkonganti@11: 
kkonganti@11: \
kkonganti@11:  
kkonganti@11: 
kkonganti@11: **CPIPES** is licensed under:
kkonganti@11: 
kkonganti@11: ```text
kkonganti@11: MIT License
kkonganti@11: 
kkonganti@11: In the U.S.A. Public Domain; elsewhere Copyright (C) 2022 Center for Food Safety and Nutrition (CFSAN)
kkonganti@11: 
kkonganti@11: Permission is hereby granted, free of charge, to any person obtaining a copy
kkonganti@11: of this software and associated documentation files (the "Software"), to deal
kkonganti@11: in the Software without restriction, including without limitation the rights
kkonganti@11: to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
kkonganti@11: copies of the Software, and to permit persons to whom the Software is
kkonganti@11: furnished to do so, subject to the following conditions:
kkonganti@11: 
kkonganti@11: The above copyright notice and this permission notice shall be included in all
kkonganti@11: copies or substantial portions of the Software.
kkonganti@11: 
kkonganti@11: THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
kkonganti@11: IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
kkonganti@11: FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
kkonganti@11: AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
kkonganti@11: LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
kkonganti@11: OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
kkonganti@11: SOFTWARE.
kkonganti@11: ```
kkonganti@11: 
kkonganti@11: \
kkonganti@11:  
kkonganti@11: 
kkonganti@11: 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@11: 
kkonganti@11: ```text
kkonganti@11: MIT License
kkonganti@11: 
kkonganti@11: Copyright (c) Philip Ewels
kkonganti@11: Copyright (c) Phil Ewels, Rickard Hammarén
kkonganti@11: 
kkonganti@11: Permission is hereby granted, free of charge, to any person obtaining a copy
kkonganti@11: of this software and associated documentation files (the "Software"), to deal
kkonganti@11: in the Software without restriction, including without limitation the rights
kkonganti@11: to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
kkonganti@11: copies of the Software, and to permit persons to whom the Software is
kkonganti@11: furnished to do so, subject to the following conditions:
kkonganti@11: 
kkonganti@11: The above copyright notice and this permission notice shall be included in all
kkonganti@11: copies or substantial portions of the Software.
kkonganti@11: 
kkonganti@11: THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
kkonganti@11: IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
kkonganti@11: FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
kkonganti@11: AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
kkonganti@11: LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
kkonganti@11: OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
kkonganti@11: SOFTWARE.
kkonganti@11: ```
kkonganti@11: 
kkonganti@11: \
kkonganti@11:  
kkonganti@11: 
kkonganti@11: The **MultiQC** report, in addition uses [DataTables](https://datatables.net), which is licensed under:
kkonganti@11: 
kkonganti@11: ```text
kkonganti@11: MIT License
kkonganti@11: 
kkonganti@11: Copyright (C) 2008-2022, SpryMedia Ltd.
kkonganti@11: 
kkonganti@11: Permission is hereby granted, free of charge, to any person obtaining a copy
kkonganti@11: of this software and associated documentation files (the "Software"), to deal
kkonganti@11: in the Software without restriction, including without limitation the rights
kkonganti@11: to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
kkonganti@11: copies of the Software, and to permit persons to whom the Software is
kkonganti@11: furnished to do so, subject to the following conditions:
kkonganti@11: 
kkonganti@11: The above copyright notice and this permission notice shall be included in all
kkonganti@11: copies or substantial portions of the Software.
kkonganti@11: 
kkonganti@11: THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
kkonganti@11: IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
kkonganti@11: FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
kkonganti@11: AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
kkonganti@11: LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
kkonganti@11: OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
kkonganti@11: SOFTWARE.
kkonganti@11: ```
kkonganti@11: 
kkonganti@11: \
kkonganti@11:  
kkonganti@11: 
kkonganti@11: The **NCBI datasets** is licensed under Public Domain.
kkonganti@11: 
kkonganti@11: ```text
kkonganti@11: # Public Domain notice
kkonganti@11: 
kkonganti@11: National Center for Biotechnology Information
kkonganti@11: 
kkonganti@11: This software is a "United States Government Work" under the terms of the
kkonganti@11: United States Copyright Act.  It was written as part of the authors'
kkonganti@11: official duties as United States Government employees and thus cannot
kkonganti@11: be copyrighted.  This software is freely available to the public for
kkonganti@11: use. The National Library of Medicine and the U.S. Government have not
kkonganti@11: placed any restriction on its use or reproduction.
kkonganti@11: 
kkonganti@11: Although all reasonable efforts have been taken to ensure the accuracy
kkonganti@11: and reliability of the software and data, the NLM and the U.S.
kkonganti@11: Government do not and cannot warrant the performance or results that
kkonganti@11: may be obtained by using this software or data. The NLM and the U.S.
kkonganti@11: Government disclaim all warranties, express or implied, including
kkonganti@11: warranties of performance, merchantability or fitness for any
kkonganti@11: particular purpose.
kkonganti@11: 
kkonganti@11: Please cite NCBI in any work or product based on this material.
kkonganti@11: ```