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CONTRIBUTING.md

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+💖:tada: Thanks for taking the time to contribute to GATK-SV! :tada:💖
+
+When it comes to open-source, every contribution makes the 
+software better for everyone and is warmly appreciated by the 
+community. To express our gratitude for your contribution, 
+we would like to provide you with easy-to-follow steps to get started.
+
+# Code of Conduct
+
+In the interest of fostering an open and welcoming environment, we as 
+contributors and maintainers pledge to make participation in our 
+project and our community a harassment-free experience for everyone, 
+regardless of age, body size, disability, ethnicity, sex characteristics, 
+gender identity and expression, level of experience, education, 
+socio-economic status, nationality, personal appearance, race, religion, 
+or sexual identity and orientation. 
+
+GATK-SV and everyone participating in it is governed by the 
+[Broad Institute Code of Conduct](https://github.com/broadinstitute/.github/blob/develop/CODE_OF_CONDUCT.md).
+By participating, you are expected to uphold this code.
+
+
+# What Should I Know Before I Get Started?
+
+GATK-SV is a _pipeline_ written in 
+[Workflow Description Language](https://openwdl.org/) (WDL) 
+that orchestrates joint genotyping structural variations using 
+open-source tools and custom scripts. The tools and scripts are distributed 
+in Docker containers, and the pipeline is executed using a 
+[Cromwell](https://cromwell.readthedocs.io/en/stable/) 
+server running on commercial cloud platforms. 
+You may interface with a Cromwell server using 
+[Cromshell](https://github.com/broadinstitute/cromshell) or 
+[Terra platform](https://terra.bio). We currently publish 
+Docker images on Google Container Registry (GCR) and Azure 
+Container Registry (work-in-progress).
+
+To study your data using the GATK-SV pipeline, please 
+refer to the [documentation](README.md) for details.
+
+# I have a question! 
+
+Please refer to the [documentation](README.md).
+If you still have questions, please start a new discussion under the 
+[Discussions](https://github.com/broadinstitute/gatk-sv/discussions) tab. 
+
+
+# How Can I Contribute?
+
+## Reporting Bugs
+
+We appreciate your bug reports; bugs are tracked as 
+[GitHub issues](https://github.com/broadinstitute/gatk-sv/issues). 
+Before submitting a bug report, please search the issues tab, 
+as you may find a similar issue reported. Please submit a 
+bug report if you do not find a similar issue.
+
+### How do I submit a bug report?
+
+The following guidelines help submit bug reports that are 
+easier to understand and reproduce by the maintainers and 
+the community and help find related reports.
+
+Use a clear and descriptive title for the issue;
+Provide a minimally reproducible example;
+Provide specific details on how the observed and expected behaviors differ.
+
+
+## Your First Code Contribution
+
+Thank you for considering code contributions to GATK-SV. 
+All code contributions to the GATK-SV repository are made through 
+[pull requests (PR)](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-pull-requests), 
+and you may take the following steps to prepare and submit your PRs.
+
+### Fork GATK-SV (one time)
+A [fork](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/working-with-forks/about-forks) 
+is your copy of a GitHub repository that you can make your changes 
+without affecting the source.
+
+You may create a fork of [broadinstitute/gatk-sv](https://github.com/broadinstitute/gatk-sv) 
+following [these instructions](https://docs.github.com/en/get-started/quickstart/fork-a-repo#forking-a-repository).
+
+### Clone GATK-SV fork (one time)
+
+Once you have forked [broadinstitute/gatk-sv](https://github.com/broadinstitute/gatk-sv), 
+you need to download your fork to your computer so you can implement any changes. 
+This process is commonly known as _clone_ing a GitHub repository. You may follow 
+[these instructions](https://docs.github.com/en/get-started/quickstart/fork-a-repo#cloning-your-forked-repository) 
+on cloning your fork of GATK-SV, or in a nutshell, you may run the following commands.
+
+Clone your fork
+```shell
+$ git clone https://github.com/YOUR_GITHUB_USERNAME/gatk-sv ./gatk-sv
+$ cd gatk-sv
+```
+
+Add a reference to `broadinstitute/gatk-sv` so you can keep your fork in synch in the future.
+
+```shell
+$ git remote add upstream https://github.com/broadinstitute/gatk-sv
+```
+
+### Create a feature branch (once per feature)
+
+In a loose sense, a [_branch_](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-branches) 
+is an isolated copy of the code in your forked repository, where the changes 
+you implement in one branch does not affect the code on the other branches. 
+It is a common practice to create one branch per each feature you would like 
+to implement, and do not implement features on the `master` branch of the repository. 
+It is mainly because you can use the `master` branch to synchronize your fork with 
+the upstream and get a fresh copy of the up-to-date codebase to start your feature development. 
+
+You may create a branch using [Github](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-and-deleting-branches-within-your-repository) 
+or [git](https://git-scm.com/book/en/v2/Git-Branching-Basic-Branching-and-Merging). 
+In a nutshell, you may create a branch as the following.
+
+Ensure you are on the `master` branch.  
+```shell
+$ git checkout master
+```
+
+Create a branch
+```shell
+$ git checkout -b YOUR-BRANCH-NAME
+```
+Synchronize your branch with `broadinstitute/gatk-sv`. 
+```shell
+$ git fetch upstream
+$ git merge upstream/master
+```
+
+Push your branch to GitHub
+```shell
+$ git push –set-upstream origin YOUR-BRANCH-NAME
+```
+### Implement a new feature or fix a bug
+
+You may open the code base in any text editor or integrated development environment (IDE). 
+We recommend using [PyCharm](https://www.jetbrains.com/pycharm/) or 
+[Visual Studio](https://visualstudio.microsoft.com/vs/community/), 
+which are both freely available. Please follow the following guidelines 
+when making changes to the codebase.
+
+- **Coding Style**: GATK-SV is composed of code written in various programming languages, 
+including WDL, Python, Bash, and R. Please follow the styling guidelines of each programming 
+language; e.g., [PEP-8](https://peps.python.org/pep-0008/) for Python.
+
+- **Documentation**: Please add concise and descriptive documentation to your changes.
+
+
+
+### Commit changes
+_Commiting_ changes means tracking them via _git_. You may submit a change in 
+one commit or split it into multiple related commits. Though there is no hard 
+rule on splitting your commits, there are 
+[best practices](https://github.blog/2022-06-30-write-better-commits-build-better-projects/) 
+that we highly recommend. In GATK-SV, we 
+[`squash and merge`](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/incorporating-changes-from-a-pull-request/about-pull-request-merges#squash-and-merge-your-commits) 
+pull requests, which squashes all the commits into a single commit and 
+merge on the `master` branch.
+
+You may commit changes to git using its command line interface (CLI) from a 
+terminal or use the graphical user interface (GUI) of the IDE you are using. 
+You may use the following command if you are using a terminal 
+(details [here](https://www.atlassian.com/git/tutorials/saving-changes/git-commit), 
+or follow the guidelines on making commits in 
+[PyCharm](https://www.jetbrains.com/help/pycharm/commit-and-push-changes.html#commit) 
+and [Visual Studio](https://learn.microsoft.com/en-us/visualstudio/version-control/git-make-commit?view=vs-2022)).
+
+```shell
+$ git commit -m "commit message"
+```
+
+### Make a pull request
+
+The commits you created are tracked on the feature branch of your fork. 
+To bring these changes to GATK-SV, you need to create a pull request. 
+You may follow these guidelines on 
+[creating a pull request](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/creating-a-pull-request?tool=webui&platform=windows). 
+When creating a pull request, please provide concise and descriptive 
+information on the expected behavior, thoroughly test your changes and 
+provide minimally reproducible steps to test your code. After your pull 
+request is reviewed and approved, your commits can be squash-committed 
+to the `master` branch of GATK-SV.
+
+
+# License
+By contributing your code to the GATK-SV GitHub repository, you agree 
+to license your contribution under the [BSD 3-Clause license](LICENSE.TXT).