kkonganti@101: # CPIPES (CFSAN PIPELINES)
kkonganti@101: 
kkonganti@101: ## The modular pipeline repository at CFSAN, FDA
kkonganti@101: 
kkonganti@101: **CPIPES** (CFSAN PIPELINES) is a collection of modular pipelines based on **NEXTFLOW**,
kkonganti@101: mostly for bioinformatics data analysis at **CFSAN, FDA.**
kkonganti@101: 
kkonganti@101: ---
kkonganti@101: 
kkonganti@101: ### **LICENSES**
kkonganti@101: 
kkonganti@101: \
kkonganti@101:  
kkonganti@101: 
kkonganti@101: **CPIPES** is licensed under:
kkonganti@101: 
kkonganti@101: ```text
kkonganti@101: MIT License
kkonganti@101: 
kkonganti@101: In the U.S.A. Public Domain; elsewhere Copyright (c) 2022 U.S. Food and Drug Administration
kkonganti@101: 
kkonganti@101: Permission is hereby granted, free of charge, to any person obtaining a copy
kkonganti@101: of this software and associated documentation files (the "Software"), to deal
kkonganti@101: in the Software without restriction, including without limitation the rights
kkonganti@101: to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
kkonganti@101: copies of the Software, and to permit persons to whom the Software is
kkonganti@101: furnished to do so, subject to the following conditions:
kkonganti@101: 
kkonganti@101: The above copyright notice and this permission notice shall be included in all
kkonganti@101: copies or substantial portions of the Software.
kkonganti@101: 
kkonganti@101: THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
kkonganti@101: IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
kkonganti@101: FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
kkonganti@101: AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
kkonganti@101: LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
kkonganti@101: OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
kkonganti@101: SOFTWARE.
kkonganti@101: ```
kkonganti@101: 
kkonganti@101: \
kkonganti@101:  
kkonganti@101: 
kkonganti@101: 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@101: 
kkonganti@101: ```text
kkonganti@101: MIT License
kkonganti@101: 
kkonganti@101: Copyright (c) Philip Ewels
kkonganti@101: Copyright (c) Phil Ewels, Rickard Hammarén
kkonganti@101: 
kkonganti@101: Permission is hereby granted, free of charge, to any person obtaining a copy
kkonganti@101: of this software and associated documentation files (the "Software"), to deal
kkonganti@101: in the Software without restriction, including without limitation the rights
kkonganti@101: to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
kkonganti@101: copies of the Software, and to permit persons to whom the Software is
kkonganti@101: furnished to do so, subject to the following conditions:
kkonganti@101: 
kkonganti@101: The above copyright notice and this permission notice shall be included in all
kkonganti@101: copies or substantial portions of the Software.
kkonganti@101: 
kkonganti@101: THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
kkonganti@101: IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
kkonganti@101: FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
kkonganti@101: AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
kkonganti@101: LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
kkonganti@101: OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
kkonganti@101: SOFTWARE.
kkonganti@101: ```
kkonganti@101: 
kkonganti@101: \
kkonganti@101:  
kkonganti@101: 
kkonganti@101: The **MultiQC** report, in addition uses [DataTables](https://datatables.net), which is licensed under:
kkonganti@101: 
kkonganti@101: ```text
kkonganti@101: MIT License
kkonganti@101: 
kkonganti@101: Copyright (C) 2008-2022, SpryMedia Ltd.
kkonganti@101: 
kkonganti@101: Permission is hereby granted, free of charge, to any person obtaining a copy
kkonganti@101: of this software and associated documentation files (the "Software"), to deal
kkonganti@101: in the Software without restriction, including without limitation the rights
kkonganti@101: to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
kkonganti@101: copies of the Software, and to permit persons to whom the Software is
kkonganti@101: furnished to do so, subject to the following conditions:
kkonganti@101: 
kkonganti@101: The above copyright notice and this permission notice shall be included in all
kkonganti@101: copies or substantial portions of the Software.
kkonganti@101: 
kkonganti@101: THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
kkonganti@101: IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
kkonganti@101: FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
kkonganti@101: AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
kkonganti@101: LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
kkonganti@101: OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
kkonganti@101: SOFTWARE.
kkonganti@101: ```