kkonganti@17: # CPIPES (CFSAN PIPELINES) kkonganti@17: kkonganti@17: ## The modular pipeline repository at CFSAN, FDA kkonganti@17: kkonganti@17: **CPIPES** (CFSAN PIPELINES) is a collection of modular pipelines based on **NEXTFLOW**, kkonganti@17: mostly for bioinformatics data analysis at **CFSAN, FDA.** kkonganti@17: kkonganti@17: --- kkonganti@17: kkonganti@17: ### **LICENSES** kkonganti@17: kkonganti@17: \ kkonganti@17:   kkonganti@17: kkonganti@17: **CPIPES** is licensed under: kkonganti@17: kkonganti@17: ```text kkonganti@17: MIT License kkonganti@17: kkonganti@17: In the U.S.A. Public Domain; elsewhere Copyright (C) 2022 Center for Food Safety and Nutrition (CFSAN) kkonganti@17: kkonganti@17: Permission is hereby granted, free of charge, to any person obtaining a copy kkonganti@17: of this software and associated documentation files (the "Software"), to deal kkonganti@17: in the Software without restriction, including without limitation the rights kkonganti@17: to use, copy, modify, merge, publish, distribute, sublicense, and/or sell kkonganti@17: copies of the Software, and to permit persons to whom the Software is kkonganti@17: furnished to do so, subject to the following conditions: kkonganti@17: kkonganti@17: The above copyright notice and this permission notice shall be included in all kkonganti@17: copies or substantial portions of the Software. kkonganti@17: kkonganti@17: THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR kkonganti@17: IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, kkonganti@17: FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE kkonganti@17: AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER kkonganti@17: LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, kkonganti@17: OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE kkonganti@17: SOFTWARE. kkonganti@17: ``` kkonganti@17: kkonganti@17: \ kkonganti@17:   kkonganti@17: kkonganti@17: 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: kkonganti@17: ```text kkonganti@17: MIT License kkonganti@17: kkonganti@17: Copyright (c) Philip Ewels kkonganti@17: Copyright (c) Phil Ewels, Rickard Hammarén kkonganti@17: kkonganti@17: Permission is hereby granted, free of charge, to any person obtaining a copy kkonganti@17: of this software and associated documentation files (the "Software"), to deal kkonganti@17: in the Software without restriction, including without limitation the rights kkonganti@17: to use, copy, modify, merge, publish, distribute, sublicense, and/or sell kkonganti@17: copies of the Software, and to permit persons to whom the Software is kkonganti@17: furnished to do so, subject to the following conditions: kkonganti@17: kkonganti@17: The above copyright notice and this permission notice shall be included in all kkonganti@17: copies or substantial portions of the Software. kkonganti@17: kkonganti@17: THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR kkonganti@17: IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, kkonganti@17: FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE kkonganti@17: AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER kkonganti@17: LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, kkonganti@17: OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE kkonganti@17: SOFTWARE. kkonganti@17: ``` kkonganti@17: kkonganti@17: \ kkonganti@17:   kkonganti@17: kkonganti@17: The **MultiQC** report, in addition uses [DataTables](https://datatables.net), which is licensed under: kkonganti@17: kkonganti@17: ```text kkonganti@17: MIT License kkonganti@17: kkonganti@17: Copyright (C) 2008-2022, SpryMedia Ltd. kkonganti@17: kkonganti@17: Permission is hereby granted, free of charge, to any person obtaining a copy kkonganti@17: of this software and associated documentation files (the "Software"), to deal kkonganti@17: in the Software without restriction, including without limitation the rights kkonganti@17: to use, copy, modify, merge, publish, distribute, sublicense, and/or sell kkonganti@17: copies of the Software, and to permit persons to whom the Software is kkonganti@17: furnished to do so, subject to the following conditions: kkonganti@17: kkonganti@17: The above copyright notice and this permission notice shall be included in all kkonganti@17: copies or substantial portions of the Software. kkonganti@17: kkonganti@17: THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR kkonganti@17: IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, kkonganti@17: FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE kkonganti@17: AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER kkonganti@17: LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, kkonganti@17: OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE kkonganti@17: SOFTWARE. kkonganti@17: ``` kkonganti@17: kkonganti@17: \ kkonganti@17:   kkonganti@17: kkonganti@17: The **NCBI datasets** is licensed under Public Domain. kkonganti@17: kkonganti@17: ```text kkonganti@17: # Public Domain notice kkonganti@17: kkonganti@17: National Center for Biotechnology Information kkonganti@17: kkonganti@17: This software is a "United States Government Work" under the terms of the kkonganti@17: United States Copyright Act. It was written as part of the authors' kkonganti@17: official duties as United States Government employees and thus cannot kkonganti@17: be copyrighted. This software is freely available to the public for kkonganti@17: use. The National Library of Medicine and the U.S. Government have not kkonganti@17: placed any restriction on its use or reproduction. kkonganti@17: kkonganti@17: Although all reasonable efforts have been taken to ensure the accuracy kkonganti@17: and reliability of the software and data, the NLM and the U.S. kkonganti@17: Government do not and cannot warrant the performance or results that kkonganti@17: may be obtained by using this software or data. The NLM and the U.S. kkonganti@17: Government disclaim all warranties, express or implied, including kkonganti@17: warranties of performance, merchantability or fitness for any kkonganti@17: particular purpose. kkonganti@17: kkonganti@17: Please cite NCBI in any work or product based on this material. kkonganti@17: ```