They have a DOI and everything! Kate Voss presented this poster at the Bioinformatics Open-Source Conference in Prague last month. See the abstract below. The full citation is:

Voss K, Gentry J and Van der Auwera G. Full-stack genomics pipelining with GATK4 + WDL + Cromwell [version 1; not peer reviewed]. F1000Research 2017, 6(ISCB Comm J):1379 (poster) (doi: 10.7490/f1000research.1114631.1)

In case you're wondering, the flying pig with warp nacelles is Jamie, the mascot of the Cromwell execution engine. And the story behind that... is a story for another time :)


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Heads up! The upcoming version 29 of Cromwell will include a breaking change in the command line syntax. Full details will be provided in the release notes when Cromwell 29 is ready for primetime; in the meantime the gist is that we're moving away from positional inputs in favor of explicit arguments. So for example this simple execution command:

java -jar Cromwell.jar run myWorkflow.wdl myWorkflow_inputs.json

will change to the more explicit:

java -jar Cromwell.jar run myWorkflow.wdl --inputs myWorkflow_inputs.json

The code changes can be viewed here for those who are into that level of detail.

We plan to update usage examples and relevant instructions in the WDL documentation materials at the time the new version is released, and will add a note regarding versions where appropriate for anyone still using a version anterior to 29. Note that there may be a short lag between the release and the documentation updates; we'll try to keep it to a minimum.

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Last week we released Cromwell 27, the latest and greatest Cromwell to date! Much of our work this quarter has been directed towards improving the general speed and scalability of Cromwell.

But before you do, have a look at the new feature highlights below!


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Cromwell 26 has a new way to deal with I/O (Input/Output) operations. This new approach reduces network load and provides better control over the resources allocated throughout the system. This blogpost will describe some of the optimizations and how they improve Cromwell stability and reliability.


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Cromwell 25 was released a few weeks ago but already Cromwell 26 is available! In this release we improved Cromwell's ability to cope with failure, including adding cases where Cromwell will retry jobs that failed due to transient errors. Note that migration from version 25 to 26 is expected to take extra time as explained further below.

But before you do, have a look at the version highlights below!


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TESting, TESting, 1 2 3...

Posted by jgentry on 20 Mar 2017 (0)


TL;DR :In Cromwell 25, we added a backend named TES to Cromwell’s portfolio, promoting the GA4GH vision of interoperability between genomic analysis tools. We exercise the TES backend using Funnel, a neat piece of software coming out of Kyle Ellrott’s group at OHSU that allows us to dispatch jobs to a variety of platforms using the same API.

The Global Alliance For Genomics & Health (aka GA4GH) is an international coalition formed to enable the sharing of genomic and clinical data in order to help unlock potential advancements in medicine and science. For the most part the GA4GH provides APIs that are implemented by frameworks and tools throughout our field. With these standardized APIs, analysts and software developers are able to take advantage of a much broader and richer ecosystem of tools than they previously were able to. But more on this later. The take home message is that now the scientific community as a whole is able to spend more time working towards bettering humanity instead of just gluing tools together.

Within the GA4GH is the Containers & Workflows (CWF) working group, which focuses on providing APIs that define generic schemes for identifying tools, submitting workflows, and submitting jobs to compute platforms (disclosure: I happen to co-chair this group). At my day job as one of the developers of Cromwell I’m interested in how we can implement these APIs to promote interoperability of different computing platforms in the bioinformatics space.


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Well, no, there isn't a Cromwell/WDL musical (yet) -- it's just that I gave a talk last night in New York, at a meetup organized by Phosphorus and hosted by FirstMark. We had a great crowd, and I have to give them mad props for listening to me go on about GATK workflows and pipelining strategies for well over the allotted hour. Especially considering I've been getting over a bout of laryngitis and my voice kept oscillating between high-pitched whine and raspy whisper... There will be a video posted on YouTube in the next few days and it would be awesome if they could get someone to do a voice dub! In the meantime, my slide deck is available here.

UPDATE: And here's the video on YouTube.


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Cromwell 25 release

Posted by KateVoss on 23 Feb 2017 (1)


Happy 25th birthday, Cromwell! You're a quarter of a century old! In this version, we added a major new feature we named "call caching" that could potentially save you tons of money; as well as labels, a TES backend and new WDL functions.

But before you do, have a look at the version highlights below!


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Announcing the WDL Blog!

Posted by KateVoss on 22 Feb 2017 (1)


WDL-away your day with us on the WDL blog! These blog posts will be geared towards developers who are looking for the nitty-gritty-codey details of WDL and Cromwell, such as new backends, parameters, etc. We'll post about new WDL documents and Cromwell releases, as well as other technical topics.

You can use your favorite RSS reader to subscribe to just the WDL Announcements category of posts. Click here for information on subscribing to WDL Announcements by email.

To subscribe via RSS to blog posts about FireCloud, click here. To subscribe via RSS to blog posts about GATK, click here.

And don't forget to follow us on Twitter!

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Cromwell v 0.21 Release

Posted by KateN on 26 Sep 2016 (0)


Cromwell version 0.21 was released on 9/23/2016. You can download the release here. See below for the release notes.


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RT @geoffjentry: We had a hackathon yesterday to make the AWS support in Cromwell. A lot of great progress was made, the next release shoul…
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