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31 changes: 31 additions & 0 deletions .github/ISSUE_TEMPLATE/bug_report.md
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---
name: Bug report
about: Create a report to help improve the Fonda
title: ''
labels: bug
assignees: ''

---

**Describe the bug**
A clear and concise description of what the bug is.

**To Reproduce**
Steps to reproduce the behavior:
1. Go to '...'
2. Click on '....'
3. Scroll down to '....'
4. See error

**Expected behavior**
A clear and concise description of what you expected to happen.

**Screenshots**
If applicable, add screenshots to help explain your problem.

**Environment:**
- OS: [e.g. CentOS]
- Version: [e.g. 2.0.0]

**Additional context**
Add any other context about the problem here.
20 changes: 20 additions & 0 deletions .github/ISSUE_TEMPLATE/feature_request.md
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---
name: Feature request
about: Request a feature implementation
title: ''
labels: enhancement
assignees: ''

---

**Background**
A clear and concise description of what the problem is. Ex. At the moment, Fonda does not allow [...] and it would be nice to [...] because [...]

**Approach**
A clear and concise description of what you want to happen.

**Other options**
A clear and concise description of any alternative solutions or features you've considered.

**Additional context**
Add any other context or screenshots about the feature request here.
32 changes: 32 additions & 0 deletions .github/PULL_REQUEST_TEMPLATE/pull_request_template.md
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# Description

Fixes #[related_issue_number]

Please include a summary of the change and which issue is fixed. Please also include relevant motivation and context. List any dependencies that are required for this change.

## Type of change

Please delete options that are not relevant.

- [ ] Bug fix (non-breaking change which fixes an issue)
- [ ] New feature (non-breaking change which adds functionality)
- [ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
- [ ] This change requires a documentation update
- [ ] This change consists of tests extending or updating

# How Has This Been Tested?

Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce.
Please also list any relevant details for your test configuration.

- Test 1
- Test 2

# Checklist:

- [ ] My code follows the style guidelines of this project
- [ ] New and existing unit and integrations tests pass locally with my changes
- [ ] I have analyzed my own code (via `PMD`, `checkstyle`, `JaCoCo`) by `./gradlew check` command
- [ ] I have commented on my code, particularly in hard-to-understand areas
- [ ] I have made corresponding changes to the documentation
- [ ] I have added tests that prove my fix is effective or that my feature works
67 changes: 66 additions & 1 deletion CONTRIBUTING.md
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#Contributing Guidelines

Thanks for your interest in Fonda. Our goal is to offer a scalable and automatic analysis of multiple NGS sequencing data types.

- [Branches management guidelines](#branches-management-guidelines)
- [CI process description](#ci-process-description)
- [Contributions](#contributions)
- [Reporting Bugs](#reporting-bugs)
- [Suggesting Enhancements](#suggesting-enhancements)
- [Pull Requests](#pull-requests)

## Branches management guidelines

* Default repository branch: `develop`. It contains all the latest changes, which are merged via the `Pull Requests`
Expand Down Expand Up @@ -75,4 +85,59 @@ fn_branch1 |
|\___________/| file transfer || _|_|_|_|_|_ || file transfer |___Browser___|
| fonda-*.zip | -----------------> || _|_|_|_|_|_ || -----------------> | |
|_____________| to S3 ||_|_|_|_|_|_|_|| to user |_____________|
```
```

## Contributions

You can get started to contribute to the Fonda in several ways by creating:
- issue: [reporting bugs](#reporting-bugs) or [suggesting enhancements](#suggesting-enhancements)
- [pull requests](#pull-requests)

**Issues** are the way to track the problems, ideas, questions that would be raised while using the code in a repository.
These can include bugs to fix, features to add, or documentation that looks outdated.
It can also be used to keep track of tasks, enhancements for the codebase.
The issue shall be discussed by repository maintainers and contributors first. If the issue is relevant and requires a solution, then it should be implemented and updated in the repository via pull request.

**Pull request** allows you made a feature implementation or a bug-fix in the code to a repository.
Maintainers can see the changes and suggest modifications in the code.
If the changes are acceptable, they can merge it to the branch requested.

### Reporting Bugs

This section guide is submitting a bug report for Fonda.

Bugs are tracked as GitHub [issues](https://github.com/epam/fonda/issues). Create an issue on the repository and provide the bug information by filling in the [template](https://github.com/epam/fonda/blob/develop/.github/ISSUE_TEMPLATE/bug_report.md).
This will keep your bugs tidy and relevant.
When you are creating a bug report, please include as many details as possible.

> **Note**: Before creating bug reports, please check the bug is not already described in existing [issues](https://github.com/epam/fonda/issues).

### Suggesting Enhancements

This section guide is submitting an enhancement suggestion for Fonda.

Enhancement suggestions are tracked as GitHub [issues](https://github.com/epam/fonda/issues).
Create an issue on the repository and provide the enhancement information by filling in the [template](https://github.com/epam/fonda/blob/develop/.github/ISSUE_TEMPLATE/feature_request.md).

### Pull Requests

This section guide is submitting an pull requests for Fonda.

Contributions to Fonda should be made in the form of GitHub pull [requests](https://github.com/epam/fonda/pulls).
Create an PR on the repository and describe the enhancement by filling in the [template](https://github.com/epam/fonda/blob/develop/.github/ISSUE_TEMPLATE/pull_request_template.md).
Each pull request will be reviewed by a core Fonda maintainers who has appropriate permissions.

Please follow these steps to have your contribution considered by the maintainers:

- Branch from the `develop` branch. If needed, rebase to the current `develop`
branch before submitting your pull request. If it doesn't merge cleanly with
master you may be asked to rebase your changes.

- Each PR should compile and pass tests.

- Each PR should pass `PMD`, `checkstyle`, `JaCoCo` checks.

- Add tests relevant to the fixed bug or new feature.


>_All code in this repository is under the Apache License, Version 2.0._