Contributing and Reporting

Contact

In order to report a bug, ask for a feature request or say hello, please fill an issue.

Contributing

Contributions are most welcome. This repository is organised as follows:

• The complete workflow is in workflow.wdl.
• All dependencies are built within a docker image defined by docker/Dockerfile.
• The "glue" code is written in Julia. Although contributions using other languages are acceptable, we prefer Julia as it keeps dependencies light and the repository clean.

Running Tests

Running the tests locally requires a set of dependencies to be installed:

• Julia
• R
• SuSiE
• METAL
• plink2
• cromwell.

The tests further assume that the environment variable CROMWELL_PATH points to the cromwell jar file.