Welcome!

Thank you for contributing to CDC's Open Source projects! If you have any questions or doubts, don't be afraid to send them our way. We appreciate all contributions, and we are looking forward to fostering an open, transparent, and collaborative environment.

Before contributing, we encourage you to read LICENSE, README, and code-of-conduct files, also found in this repository. If you have any inquiries or questions not answered by the content of this repository, feel free to contact us.

We highly encourage collaboration and welcome feedback on CDC’s PHoeNix pipeline. However, if you choose to fork the PHoeNix pipeline, you are assuming responsibility for that new fork. The DHQP Clinical and Environmental Microbiology Branch does not guarantee the performance or results of any pipelines or scripts that have been forked or copied from this repo.

This project 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 project will be released under the CC0 dedication. By submitting a pull request you are agreeing to comply with this waiver of copyright interest.

Requesting Changes

Our pull request/merging process is designed to give the CDC PHoeNIx Team and others in our space an opportunity to consider and discuss any suggested changes. This policy affects all CDC spaces, both on-line and off, and all users are expected to abide by it.

Open an issue in the repository

If you don't have specific language (code) to submit, but would like to suggest a change or report a bug, you can open an issue in this repository. Team members will respond to the issue as soon as possible.

When submitting an issue, please provide a reproducible example that will allow someone else to recreate your problem.

There are some things you need to include to make your example reproducible:

1. What environment you are running the pipeline (i.e. HPC, local, cloud etc) in
2. What version of the pipeline you are using
3. The command that was run to cause the error
   • If you used a custom config file please provide it
4. The text of the error itself - screen shots are great for this!
5. Include the files that caused the error (if the files contain sensitive information (PII), email [email protected] with the Subject "PHX ISSUE #" BEFORE sharing anything to discuss appropriate next steps).
6. If you have done any internet sleuthing already please link to any relevant posts on the topic.

Submit a pull request

If you would like to contribute code, please submit a pull request. In order for us to merge a pull request, it must:

• Be at least seven days old. Pull requests may be held longer if necessary to give people the opportunity to assess it.
• Receive a +1 from a majority of team members associated with the request. If there is significant dissent between the team, a meeting will be held to discuss a plan of action for the pull request.

If you are thinking of submitting code for a feature please reach out before hand and let the team know via slack or email ([email protected]).

For further information or help, don't hesitate to get in touch on the Slack #phoenix-dev channel.