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1 # CPIPES (CFSAN PIPELINES)
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2
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3 ## The modular pipeline repository at CFSAN, FDA
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4
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5 **CPIPES** (CFSAN PIPELINES) is a collection of modular pipelines based on **NEXTFLOW**,
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6 mostly for bioinformatics data analysis at **CFSAN, FDA.**
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7
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8 ---
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9
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10 ### **LICENSES**
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11
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12 \
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13
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14
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15 **CPIPES** is licensed under:
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16
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17 ```text
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18 MIT License
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19
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20 In the U.S.A. Public Domain; elsewhere Copyright (C) 2022 Center for Food Safety and Nutrition (CFSAN)
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21
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22 Permission is hereby granted, free of charge, to any person obtaining a copy
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23 of this software and associated documentation files (the "Software"), to deal
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24 in the Software without restriction, including without limitation the rights
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25 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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26 copies of the Software, and to permit persons to whom the Software is
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27 furnished to do so, subject to the following conditions:
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28
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29 The above copyright notice and this permission notice shall be included in all
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30 copies or substantial portions of the Software.
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31
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32 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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33 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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34 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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35 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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36 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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37 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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38 SOFTWARE.
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39 ```
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40
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41 \
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42
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43
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44 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:
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45
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46 ```text
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47 MIT License
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48
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49 Copyright (c) Philip Ewels
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50 Copyright (c) Phil Ewels, Rickard Hammarén
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51
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52 Permission is hereby granted, free of charge, to any person obtaining a copy
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53 of this software and associated documentation files (the "Software"), to deal
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54 in the Software without restriction, including without limitation the rights
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55 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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56 copies of the Software, and to permit persons to whom the Software is
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57 furnished to do so, subject to the following conditions:
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58
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59 The above copyright notice and this permission notice shall be included in all
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60 copies or substantial portions of the Software.
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61
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62 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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63 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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64 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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65 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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66 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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67 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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68 SOFTWARE.
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69 ```
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70
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71 \
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72
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73
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74 The **MultiQC** report, in addition uses [DataTables](https://datatables.net), which is licensed under:
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75
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76 ```text
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77 MIT License
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78
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79 Copyright (C) 2008-2022, SpryMedia Ltd.
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80
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81 Permission is hereby granted, free of charge, to any person obtaining a copy
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82 of this software and associated documentation files (the "Software"), to deal
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83 in the Software without restriction, including without limitation the rights
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84 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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85 copies of the Software, and to permit persons to whom the Software is
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86 furnished to do so, subject to the following conditions:
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87
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88 The above copyright notice and this permission notice shall be included in all
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89 copies or substantial portions of the Software.
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90
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91 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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92 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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93 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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94 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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95 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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96 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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97 SOFTWARE.
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98 ```
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99
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100 \
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101
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102
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103 The **NCBI datasets** is licensed under Public Domain.
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104
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105 ```text
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106 # Public Domain notice
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107
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108 National Center for Biotechnology Information
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109
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110 This software is a "United States Government Work" under the terms of the
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111 United States Copyright Act. It was written as part of the authors'
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112 official duties as United States Government employees and thus cannot
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113 be copyrighted. This software is freely available to the public for
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114 use. The National Library of Medicine and the U.S. Government have not
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115 placed any restriction on its use or reproduction.
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116
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117 Although all reasonable efforts have been taken to ensure the accuracy
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118 and reliability of the software and data, the NLM and the U.S.
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119 Government do not and cannot warrant the performance or results that
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120 may be obtained by using this software or data. The NLM and the U.S.
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121 Government disclaim all warranties, express or implied, including
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122 warranties of performance, merchantability or fitness for any
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123 particular purpose.
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124
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125 Please cite NCBI in any work or product based on this material.
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126 ```
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