# wgbs-pipeline

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## Overview

An [ENCODE](https://www.encodeproject.org/) pipeline for processing whole-genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS) data using [gemBS](https://github.com/heathsc/gemBS) for alignment and methylation extraction.

## Installation

1. Git clone this pipeline.
    ```bash
    $ git clone https://github.com/ENCODE-DCC/wgbs-pipeline
    ```

2. Install [Caper](https://github.com/ENCODE-DCC/caper), requires `java` >= 1.8, `docker`, and `python` >= 3.6 . Caper is a python wrapper for [Cromwell](https://github.com/broadinstitute/cromwell).
    ```bash
    $ pip install caper  # use pip3 if it doesn't work
    ```

3. Follow [Caper's README](https://github.com/ENCODE-DCC/caper) carefully to configure it for your platform (local, cloud, cluster, etc.)
> **IMPORTANT**: Configure your Caper configuration file `~/.caper/default.conf` correctly for your platform.

## Usage

To verify your installation, you can run the following pipeline with a test data set by invoking the following command from the root of the cloned repository.

> Note: this will incur some cost when running in cloud environments.

```bash
$ caper run wgbs-pipeline.wdl -i tests/functional/json/test_wgbs.json --docker
```

For detailed usage, see [usage](docs/usage.md)

## Inputs

See [inputs](docs/reference.md#inputs)


## Outputs

See [outputs](docs/reference.md#outputs)

## Contributing

We welcome comments, questions, suggestions, bug reports, feature requests, and pull requests (PRs). Please use one of the existing Github issue templates if applicable. When contributing code, please follow the [Developer Guidelines](docs/CONTRIBUTING.md#developer-guidelines).