Pipelining with workflows

Allie Hajian
  • Updated

An introduction to workflows - one of two analysis modes you can use on the Terra platform. Workflows (aka pipelines) are a series of steps performed by an external compute engine - often used for automated, bulk analysis (such as aligning genomic reads). Pipelines run on Terra are written in Workflow Description Language (WDL), a workflow processing language that is easy for humans to read and write. 

What you need to run a workflow (pipeline) in a Terra workspace "Can compute" access to the workspace  
You need permission to do any operations that have a GCP cost (i.e. run workflows) in a
workspace. You can do this if someone shares a workspace with you as "can-compute
writer." If you create or copy a workspace using your own Billing project, you are the owner, by default, and can run workflows. 
One or more workflows
If you clone a Workspace that already contains workflows, these will be in your copy
as well. If the Workflows tab of your workspace is empty, you can import workflows
from the Terra library's code and workflows section. 
Input data
Input data files can be located in the workspace Google bucket, or linked to the
workspace by metadata in the data table.

Practice pipelining with the Workflows Quickstart

One way to get up and running quickly is to clone and run the workflows in a featured workspace. The Workflows Quickstart tutorial includes everything you need to get hands on running workflows.

Tutorial workspace | Step-by-step guide

Copy the Terra Workflows Quickstart workspace to your own billing account and work through the three exercises.

Part 1 - Run a preconfigured workflow on a single sample from the Workflows pageWorkflows-QuickStart_Part1_flow.png

Part 2 - Set up and run a workflow on two samples (you'll create a set in the process)Workflows-QuickStart_Part2_flow.png

Part 3 - Run downstream analysis on a set of samples Workflows-QuickStart_Part3_flow.png

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