You may have noticed we’ve been talking about this new thing called WDL--the Workflow Definition Language. We've published a tutorial using WDL to run some GATK tasks, as well as a pipeline implementation of the Best Practices for germline short variant discovery written in WDL. These fully-baked WDL scripts assume you already know what to do with them, but you may be wondering where to start. Whether you need a few pointers to get you started, or you’re completely new to this, we’ve got you covered. (And if you’re just looking for how to run pre-written WDLs, head on over to the executions section. You can still learn a lot from reading the rest of this article too though!)

WDL is designed to be easy to use--"human readable and writable" is our promise. You should think of building a pipeline with WDL like building with legos. The final product (like that full pipeline script I linked before) can look quite complex, but it is a simple matter of going step by step with your WDL building blocks.

I would recommend that you get started by reading our user guide. By reading through and clicking to the next article at the bottom of each page, the user guide will introduce you to all the pieces you can use in your lego-pipeline--from what pieces you'll need all the way through how to test & run your pipeline once you've finished it.

Once you've got a handle on what WDL can do, head over to the tutorials section. In these sequential tutorials, I walk you through how to use those building blocks to implement a small part of the GATK pipeline. Each tutorial builds on the previous one to help you learn to use WDL in new ways without repeating all of your earlier work.

You've read the user guide and you've run through the tutorials; you now have all you need to get started writing your very own WDLs. If you get stuck on something, you can always see how we do things in these real WDL scripts. If you have a more specific question, don't hesitate to post it on our WDL forum. Happy building!



Comment on this article


- Recent posts


- Upcoming events

See Events calendar for full list and dates


- Recent events

See Events calendar for full list and dates



- Follow us on Twitter

GATK Dev Team

@gatk_dev

@wbsimey Happy to hear you’ve found the resources we provide helpful!
30 Jul 19
New crop of GATK workshop videos now available on YouTube! Updated for the GATK4/2019 version of the Best Practices… https://t.co/Wfgq5YKBFg
25 Jul 19
Don't miss this #GATK workshop -- we've got a great crew lined up and the location isn't half bad either :) https://t.co/b0fL8ZLwzn
23 Jul 19
@Brunods1001 It’s been updated to use GATK4, which addresses the invalid bam output issue that affected the GATK3 v… https://t.co/AUlbjmHKmm
11 Jul 19
Wrapping up the #GATK workshop in Cambridge, UK -- it's been a blast. Great group of participants and fantastic hos… https://t.co/bvwGTU7lYq
11 Jul 19

- Our favorite tweets from others

In spite of their stated mission to support human health through genomics, many GATK pipelines are applicable to no… https://t.co/FKQTouZjbv
29 Jul 19
Me: driving myself insane over what data to keep and what to not bother with for thesis and also frantically trying… https://t.co/er2klIcw5i
18 Jul 19
@RareSeas first attempt at teaching the GATK course, do I look puzzled up there? https://t.co/4mqkHbWJy4
11 Jul 19
Can you spot CDGP PhD student, Dr. Alice Denyer, brushing up on the latest bioinformatics tools from @gatk_dev? The… https://t.co/KAbdlWLbcb
10 Jul 19
GATK workshop materials available online! Learn it in your own time with @ProjectJupyter notebooks. ^MT https://t.co/IKDa6SGwaU
8 Jul 19

See more of our favorite tweets...