:fire::bird::fire: PHoeNIx

🚨🚧 This software is currently under active development and states not part of the beta testing are advised to use with caution as it is likely to change often until there is an offical stable release (estimated early Sep 2022). 🚧🚨

For full documentation on the pipeline see the Wiki, but quick start instructions are provided below if you are feeling brave.

Quick Start

Make sure you are in the 1.0.0-dev branch:

1. Install Nextflow (>=21.10.3). This will require a version of Anaconda to be installed on your system.

   console mamba create -n nextflow -c bioconda -c conda-forge nf-core=2.2 nextflow=21.10.6 git=2.35.0 openjdk=8.0.312 graphviz

2. Install Docker or Singularity for full pipeline reproducibility.

3. Clone the PHoeNIx Repository from GitHub.

   console git clone https://github.com/CDCgov/phoenix

4. Unzip mash sketch in assets folder:

console gunzip phoenix/assets/databases/REFSEQ_20210820_Bacteria_complete.msh.gz

1. Email HAISeq@cdc.gov, with the subject line "krakenDB invite request" to request access to the sharefile link and provide the email address to send invite to.

2. Download the hash.k2d file needed for kraken2 from the CDC sharefile link. At this time this is not downloadable via command line . You will need to downloaded the file and place it into into the databases directory, $PATH_TO_CLONED_REPO/assets/databases.

Here the $PATH_TO_CLONED_REPO needs to be changed to your correct path.

1. Activate the nextflow environment with:
   

console conda activate nextflow

1. Run PHoeNIx on a test sample loaded with the package with a single command:

   console nextflow run $PATH_TO_CLONED_REPO/phoenix/main.nf -profile <singularity/docker/custom>,test

Note that we aren't cloning (downloading) the repo with this command just pulling directly. See wiki for how to clone and have the software locally.

> * 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.

1. Start running your own analysis with a samplesheet!

   console nextflow run phoenix/main.nf -profile <singularity/docker/custom> --input <path_to_samplesheet.csv>

CDCgov GitHub Organization Open Source Project

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.

Access Request, Repo Creation Request

• 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.]

Related documents

• Open Practices
• Rules of Behavior
• Thanks and Acknowledgements
• Disclaimer
• Contribution Notice
• Code of Conduct

Overview

Describe the purpose of your project. Add additional sections as necessary to help collaborators and potential collaborators understand and use your project.

Public Domain Standard Notice

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.

License Standard Notice

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.

Privacy Standard Notice

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.

Contributing Standard Notice

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.

Records Management Standard Notice

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.

Additional Standard Notices

Please refer to CDC's Template Repository for more information about contributing to this repository, public domain notices and disclaimers, and code of conduct.