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Merge pull request #42 from SchlossLab/community
Add community docs
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‎.github/CODE_OF_CONDUCT.md

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# Contributor Covenant Code of Conduct
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This document was adapted from the [Tidyverse Code of Conduct](https://tidyverse.tidyverse.org/CODE_OF_CONDUCT.html).
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## Our Pledge
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We as members, contributors, and leaders pledge to make participation in our
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community a harassment-free experience for everyone, regardless of age, body
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size, visible or invisible disability, ethnicity, sex characteristics, gender
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identity and expression, level of experience, education, socio-economic status,
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nationality, personal appearance, race, religion, or sexual identity and
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orientation.
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We pledge to act and interact in ways that contribute to an open, welcoming,
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diverse, inclusive, and healthy community.
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## Our Standards
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Examples of behavior that contributes to a positive environment for our
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community include:
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* Demonstrating empathy and kindness toward other people
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* Being respectful of differing opinions, viewpoints, and experiences
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* Giving and gracefully accepting constructive feedback
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* Accepting responsibility and apologizing to those affected by our mistakes,
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and learning from the experience
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* Focusing on what is best not just for us as individuals, but for the overall
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community
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Examples of unacceptable behavior include:
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* The use of sexualized language or imagery, and sexual attention or
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advances of any kind
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* Trolling, insulting or derogatory comments, and personal or political attacks
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* Public or private harassment
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* Publishing others' private information, such as a physical or email
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address, without their explicit permission
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* Other conduct which could reasonably be considered inappropriate in a
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professional setting
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## Enforcement Responsibilities
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Community leaders are responsible for clarifying and enforcing our standards
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of acceptable behavior and will take appropriate and fair corrective action in
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response to any behavior that they deem inappropriate, threatening, offensive,
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or harmful.
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Community leaders have the right and responsibility to remove, edit, or reject
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comments, commits, code, wiki edits, issues, and other contributions that are
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not aligned to this Code of Conduct, and will communicate reasons for moderation
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decisions when appropriate.
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## Scope
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This Code of Conduct applies within all community spaces, and also applies
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when an individual is officially representing the community in public spaces.
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Examples of representing our community include using an official e-mail
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address, posting via an official social media account, or acting as an appointed
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representative at an online or offline event.
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## Enforcement
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Instances of abusive, harassing, or otherwise unacceptable behavior may be
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reported to the community leaders responsible for enforcement
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([Pat Schloss](mailto:pschloss@umich.edu)).
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All complaints will be reviewed and investigated promptly and fairly.
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All community leaders are obligated to respect the privacy and security of the
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reporter of any incident.
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## Enforcement Guidelines
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Community leaders will follow these Community Impact Guidelines in determining
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the consequences for any action they deem in violation of this Code of Conduct:
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### 1. Correction
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**Community Impact**: Use of inappropriate language or other behavior deemed
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unprofessional or unwelcome in the community.
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**Consequence**: A private, written warning from community leaders, providing
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clarity around the nature of the violation and an explanation of why the
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behavior was inappropriate. A public apology may be requested.
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### 2. Warning
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**Community Impact**: A violation through a single incident or series of
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actions.
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**Consequence**: A warning with consequences for continued behavior. No
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interaction with the people involved, including unsolicited interaction with
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those enforcing the Code of Conduct, for a specified period of time. This
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includes avoiding interactions in community spaces as well as external channels
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like social media. Violating these terms may lead to a temporary or permanent
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ban.
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### 3. Temporary Ban
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**Community Impact**: A serious violation of community standards, including
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sustained inappropriate behavior.
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**Consequence**: A temporary ban from any sort of interaction or public
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communication with the community for a specified period of time. No public or
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private interaction with the people involved, including unsolicited interaction
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with those enforcing the Code of Conduct, is allowed during this period.
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Violating these terms may lead to a permanent ban.
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### 4. Permanent Ban
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**Community Impact**: Demonstrating a pattern of violation of community
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standards, including sustained inappropriate behavior, harassment of an
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individual, or aggression toward or disparagement of classes of individuals.
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**Consequence**: A permanent ban from any sort of public interaction within the
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community.
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## Attribution
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This Code of Conduct is adapted from the [Contributor Covenant][homepage],
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version 2.0,
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available at https://www.contributor-covenant.org/version/2/0/
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code_of_conduct.html.
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Community Impact Guidelines were inspired by [Mozilla's code of conduct
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enforcement ladder](https://github.com/mozilla/diversity).
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[homepage]: https://www.contributor-covenant.org
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For answers to common questions about this code of conduct, see the FAQ at
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https://www.contributor-covenant.org/faq. Translations are available at https://
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www.contributor-covenant.org/translations.

‎.github/CONTRIBUTING.md

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# Contributing to mikropml
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This document was adapted from the [Tidyverse Contributing guide](https://tidyverse.tidyverse.org/CONTRIBUTING.html).
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## Fixing typos
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You can fix typos, spelling mistakes, or grammatical errors in the documentation
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directly using the GitHub web interface, as long as the changes are made in the
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_source_ file.
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## Bigger changes
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If you want to make a bigger change, it's a good idea to first file an issue and make sure someone from the team agrees that it's needed.
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If you've found a bug, please file an issue that illustrates the bug with a minimal
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[reprex](https://www.tidyverse.org/help/#reprex) (this will also help you write a unit test, if needed).
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### Pull request process
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* Fork the repo and clone onto your computer.
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* Install all [conda and
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mamba](https://mamba.readthedocs.io/en/latest/installation.html) if you
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don't already have them.
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* Create a Git branch for your pull request (PR).
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* Make your changes, commit to git, and then create a PR.
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The title of your PR should briefly describe the change.
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The body of your PR should contain `Fixes #issue-number`.
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## Code of Conduct
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Please note that the mikropml-snakemake-workflow project is released with a
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[Contributor Code of Conduct](CODE_OF_CONDUCT.md). By contributing to this
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project you agree to abide by its terms.

‎.github/SUPPORT.md

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# Getting help with mikropml-snakemake-workflow
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Thanks for using mikropml-snakemake-workflow!
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Before filing an issue, there are a few places to explore and pieces to put together to make the process as smooth as possible.
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## Where to ask?
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* If it's a question: start with [Discussions](https://github.com/SchlossLab/mikropml-snakemake-workflow/discussions), and/or StackOverflow.
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* If it's a bug: you're in the right place, [file an issue](https://github.com/SchlossLab/mikropml-snakemake-workflow/issues/new).
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* If you're not sure: let the community help you figure it out by first asking
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in Discussions!
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If your problem _is_ a bug or a feature request, you can easily return here and report it.
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Before opening a new issue, be sure to [search issues and pull requests](https://github.com/SchlossLab/mikropml-snakemake-workflow/issues) to make sure the bug hasn't been reported and/or already fixed in the development version.
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By default, the search will be pre-populated with `is:issue is:open`.
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You can [edit the qualifiers](https://help.github.com/articles/searching-issues-and-pull-requests/) (e.g. `is:pr`, `is:closed`) as needed.
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For example, you'd simply remove `is:open` to search _all_ issues in the repo, open or closed.
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## What happens next?
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To be as efficient as possible, development of our software tends to be very bursty, so you shouldn't worry if you don't get an immediate response.
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Typically we don't look at a repo until a sufficient quantity of issues accumulates, then there's a burst of intense activity as we focus our efforts.
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That makes development more efficient because it avoids expensive context switching between problems, at the cost of taking longer to get back to you.
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This process makes a good reprex particularly important because it might be multiple months between your initial report and when we start working on it.
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If we can't reproduce the bug, we can't fix it!

‎.github/issue_template.md

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about: Describe a bug you've seen or make a case for a new feature
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---
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Please briefly describe your problem and what output you expect. If you have a question, please don't use this form. Instead, ask on <https://stackoverflow.com/> or <https://github.com/SchlossLab/mikropml-snakemake-workflow/discussions/21>.
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Please briefly describe your problem and what output you expect.
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If you have a question, please don't use this form.
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Instead, ask on <https://stackoverflow.com/> or
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<https://github.com/SchlossLab/mikropml-snakemake-workflow/discussions/>.
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Please include a minimal reproducible example (AKA a reprex). If you've never heard of a [reprex](http://reprex.tidyverse.org/) before, start by reading <https://www.tidyverse.org/help/#reprex>.
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Please include a minimal reproducible example (AKA a reprex). If you've never
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heard of a [reprex](http://reprex.tidyverse.org/) before, start by reading
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<https://www.tidyverse.org/help/#reprex>.
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Please include all Snakefiles and scripts used to reproduce the issue.
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If your issue is solely with mikropml and not the accompanying Snakemake
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workflow, open your issue at [the mikropml
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repo](https://github.com/SchlossLab/mikropml) instead.
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Brief description of the problem
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```r
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# insert reprex here
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```
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Brief description of the problem:

‎README.md

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Alternatively, you can download this repo and modify the code
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directly to suit your needs. See instructions [here](/quick-start.md).
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## Help & Contributing
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If you come across a bug, [open an
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issue](https://github.com/SchlossLab/mikropml-snakemake-workflow/issues)
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and include a minimal reproducible example.
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If you have questions, create a new post in
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[Discussions](https://github.com/SchlossLab/mikropml-snakemake-workflow/discussions).
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If you’d like to contribute, see our guidelines
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[here](.github/CONTRIBUTING.md).
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## Code of Conduct
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Please note that the mikropml-snakemake-workflow is released with a
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[Contributor Code of Conduct](.github/CODE_OF_CONDUCT.md).
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By contributing to this project, you agree to abide by its terms.
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## More resources
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- [mikropml docs](http://www.schlosslab.org/mikropml/)

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