Workflow management is quickly becoming a central aspect of doing bioinformatics as the field strives towards a more collaborative and reproducible approach to research. In an effort to bring genomics to the cloud, the Broad Institute (of GATK fame) developed their own workflow language, WDL, which has since morphed into a growing community-driven open source project named OpenWDL (openwdl.org). The workshop is an introduction to WDL aimed at giving researchers the necessary base knowledge to understand existing scripts, modify them or create new ones to address specific needs both in genomics and in the wider bioinformatics field. For students and researchers looking to enhance their current or future pipelines with a versatile workflow language or wanting to explore alternatives to existing workflow managers (such as CWL, Snakemake or NextFlow), this WDL crash-course is a great starting point.
(This course is also a useful primer for anyone considering doing genomics in the cloud using the platform Terra, though this will only be briefly discussed).
In this course we will cover:
The basic syntax of a workflow in WDL: variable types, calls, tasks and how commands and programs arerun within each task.
Creating a simple linearchain of tasks in WDL and running it using the very portable Cromwell executionengine
Using WOMtool to check forworkflow errors and represent workflows as simple diagrams
Generating and using JSONfiles to assign input variables for script reusability
Running time-intensive tasksin parallel using WDL’s scatter-gather approach
A very quick introduction toWDL in the cloud on the Broad Institute’s genomics platform Terra
Intended Audience
Students and researchers intending to build more efficient workflows (i.e. moving away from collections of disjointed bash scripts) or wanting to explore alternatives to existing workflow management systems (e.g. CWL, Snakemake, Nextflow).
Format
Online via Teams. Each session will combine presentation and practical with participants expected to go through coding examples and exercises at the same time as the instructor. Further exercises will be provided for practice after the session.
