An ENCODE pipeline for processing whole-genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS) data using gemBS for alignment and methylation extraction.

1. Git clone this pipeline.

   $ git clone https://github.com/ENCODE-DCC/wgbs-pipeline

2. Install Caper, requires java >= 1.8, docker, and python >= 3.6 . Caper is a python wrapper for Cromwell.

   $ pip install caper  # use pip3 if it doesn't work

3. Follow Caper's README carefully to configure it for your platform (local, cloud, cluster, etc.)

IMPORTANT: Configure your Caper configuration file ~/.caper/default.conf correctly for your platform.

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.

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

For detailed usage, see usage

See inputs

See outputs

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.