For full documentation on the pipeline see the Wiki, but quick start instructions are provided below if you are feeling brave.
-
Install
Nextflow(>=21.10.3).There are several options for install if you do not already have it on your system:
-
Install into conda environment, which will require a version of Anaconda to be installed on your system.
mamba create -n nextflow -c bioconda nextflow=21.10.6 -
If you prefer a to use
curlorwgetfor install see the Nextflow Documentation
-
-
Install
DockerorSingularity >=3.8.0for full pipeline reproducibility. -
For PHoeNIx >=2.0.0 you will need to download the public Standard-8 version kraken2 database created on or after March 14th, 2023 from Ben Langmead's github page. You CANNOT use an older version of the public kraken databases on Ben Langmead's github page. We thank @BenLangmead and @jenniferlu717 for taking the time to include an extra file in public kraken databases created after March 14th, 2023 to allow them to work in PHoeNIx! You CANNOT use the old database downloaded from CDC’s sharefile. The pipeline is not backwards compatible (hence the bump to version 2).
-
(optional) If you installed nextflow via a conda environment activate the nextflow environment with:
conda activate <environment name> -
Run PHoeNIx on a test sample loaded with the package with a single command:
nextflow run cdcgov/phoenix -r v2.0.0 -profile <singularity/docker/custom>,test -entry PHOENIX --kraken2db $PATH_TO_DB
Note that this command clones (downloading) the repo to ~/.nextflow/assets/cdcgov/phoenix. See wiki for how to clone and have the software downloaded to a different location.
> * The pipeline comes with config profiles called `docker` and `singularity` which instruct the pipeline to use the named tool for software management. For example, `-profile test,docker`.
> * Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile <institute>` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment.
-
Start running your own analysis with a samplesheet!
nextflow run cdcgov/phoenix -r v2.0.0 -profile <singularity/docker/custom> -entry PHOENIX --input <path_to_samplesheet.csv> --kraken2db $PATH_TO_DB
General disclaimer This repository was created for use by CDC programs to collaborate on public health related projects in support of the CDC mission. GitHub is not hosted by the CDC, but is a third party website used by CDC and its partners to share information and collaborate on software. CDC use of GitHub does not imply an endorsement of any one particular service, product, or enterprise.
- CDC GitHub Open Project Request Form [Requires a CDC Office365 login, if you do not have a CDC Office365 please ask a friend who does to submit the request on your behalf. If you're looking for access to the CDCEnt private organization, please use the GitHub Enterprise Cloud Access Request form.]
- Open Practices
- Rules of Behavior
- Thanks and Acknowledgements
- Disclaimer
- Contribution Notice
- Code of Conduct
Describe the purpose of your project. Add additional sections as necessary to help collaborators and potential collaborators understand and use your project.
This repository constitutes a work of the United States Government and is not subject to domestic copyright protection under 17 USC § 105. This repository is in the public domain within the United States, and copyright and related rights in the work worldwide are waived through the CC0 1.0 Universal public domain dedication. All contributions to this repository will be released under the CC0 dedication. By submitting a pull request you are agreeing to comply with this waiver of copyright interest.
The repository utilizes code licensed under the terms of the Apache Software License and therefore is licensed under ASL v2 or later.
This source code in this repository is free: you can redistribute it and/or modify it under the terms of the Apache Software License version 2, or (at your option) any later version.
This source code in this repository is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache Software License for more details.
You should have received a copy of the Apache Software License along with this program. If not, see http://www.apache.org/licenses/LICENSE-2.0.html
The source code forked from other open source projects will inherit its license.
This repository contains only non-sensitive, publicly available data and information. All material and community participation is covered by the Disclaimer and Code of Conduct. For more information about CDC's privacy policy, please visit http://www.cdc.gov/other/privacy.html.
Anyone is encouraged to contribute to the repository by forking and submitting a pull request. (If you are new to GitHub, you might start with a basic tutorial.) By contributing to this project, you grant a world-wide, royalty-free, perpetual, irrevocable, non-exclusive, transferable license to all users under the terms of the Apache Software License v2 or later.
All comments, messages, pull requests, and other submissions received through CDC including this GitHub page may be subject to applicable federal law, including but not limited to the Federal Records Act, and may be archived. Learn more at http://www.cdc.gov/other/privacy.html.
This repository is not a source of government records, but is a copy to increase collaboration and collaborative potential. All government records will be published through the CDC web site.
Please refer to CDC's Template Repository for more information about contributing to this repository, public domain notices and disclaimers, and code of conduct.