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. 

Overview: Workflows versus interactive analysis

How do you choose which analysis mode to use? It depends on your use-case - in particular whether your analysis can be automated to run in the background or needs interaction to run. 

Three reasons to use a workflow instead of an interactive analysis 1. You want to run multiple tools/commands in a specific order
2. You want to be able to run it multiple times in the same way (maybe with a few parameter changes)
3. You want to run something that takes a long time and doesn't require your input once it's running

If you can determine up front all the inputs /parameter values that need to be applied, and you want to be able to hit play and go out for lunch, use a workflow.

What do you need to run a workflow in a Terra workspace?

To run a workflow (pipeline) in a Terra workspace requires the following. 

"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 (WDLs)

If you clone a workspace that already contains workflows (see Showcase workspaces in the Library), these tools will be in your copy as well. If the Workflows tab of your workspace is empty, you can import workflows from the Terra library (code and workflows section).

Input data

Input data files can be located in the workspace Google bucket or an external bucket or data repository, and linked to the workspace by metadata in the data table.

What happens when you run a workflow in Terra?

A workflow in its simplest form is a task consisting of:

  • Path(s) of input files to read from Cloud Storage
  • A Docker image to run
  • Commands (the workflow) to run in the Docker image
  • Cloud resources to use (number of CPUs, amount of memory, disk size and type)
  • Path(s) of output files/directories to write to Cloud Storage

To run a workflow in Terra, you will:

  • Specify the path(s) of input files from Cloud Storage
  • Specify compute parameters (disk size, cost-saving options, etc.)
  • Submit workflow to Terra

Behind the scenes, Terra takes care of the details:

  • Terra communicates with GCP to set up the container (Docker) to run the workflow code.
  • Terra sends the built-in Cromwell server a packet of information containing the workflow code and inputs.
  • Cromwell - a Workflow Management System geared towards scientific workflows - parses the workflow and starts dispatching individual jobs to PAPI (the Pipelines API).
  • PAPI executes the tasks on the Google Compute Engine (GCE) and writes the output to the Workspace bucket.

The Pipelines API will:

  • Create a Compute Engine virtual machine
  • Download the container (i.e. Docker) image
  • Download the input files
  • Run a new Docker container with the specified image and command
  • Upload the output files
  • Destroy the Compute Engine virtual machine

Overview of workflow submission in Terra from Genomics in the Cloud" by Geraldine A. Van der Auwera and Brian D. O'Connor (O'Reilly press)

Bonus: What are Cromwell and PAPI?Cromwell is an open source (BSD 3-clause) execution engine written in Java that supports running WDL on three types of platforms: local machine (e.g. your laptop), a local cluster/compute farm accessed via a job scheduler (e.g. GridEngine) or a cloud platform (e.g. Google Cloud or Amazon AWS).

Pipelines API (aka "PAPI") is a GCP service that provides an easy way to launch and monitor tasks running in the cloud.

Practice pipelining with the Workflows Quickstart

One way to get up and running quickly is to clone and run the workflows in a featured Showcase workspace. The Workflows Quickstart tutorial is a self-guided tutorial that includes everything you need to get hands-on running workflows. Copy the Terra Workflows Quickstart workspace to your own billing account and work through the three exercises following the step-by-step guide

Tutorial workspace | Step-by-step guide

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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