WDL or CWL

[Pieter Lukasse]

Hi,

I'm trying to infer from sources like https://cromwell.readthedocs.io/en/stable/LanguageSupport/ , https://github.com/broadinstitute/cromwell/tree/develop and https://github.com/openwdl/wdl what the future direction will be when it comes to supporting WDL and/or CWL. I don't see a lot of activity in the WDL repos...should I assume it is not being worked on anymore? 

Thanks,

Pieter

[Lon Blauvelt]

The last commit on openwdl was made by Jeff Gentry who has left the employ of the Broad, so I'm assuming that's the case.

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[Patrick Magee]

Hello Pieter,

WDL is certainly not dead  and is actively being developed! Additionally it is the original workflow language of Cromwell (it is the language originally created for cromwell) and has first class support there! Almost all of the example workflows published by the broad are written in WDL (version 1.0).

Additionally there are some great projects being developed to help with community adoption such as MiniWDL https://github.com/chanzuckerberg/miniwdl, BioWDL https://github.com/biowdl as well as repositories like Dockstore https://dockstore.org/, The community is very much alive, and we are driving towards a major 2.0 release. At the moment, we are reviewing our RFC process and trying to come up with ways to make it easier for engines to implement the various features. I highly encourage you to get involve in any of the projects I mentioned above, to help develop features!

- Patrick

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Patrick Magee Software Developer at DNAstack T: +1-613-545-5315 dnastack.com @DNAstack

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[Patrick Magee]

Hello Lon,

I just would like to point out that WDL is no longer under the purview of the Broad, and while Jeff is no longer working at the broad, he is still involved in the broader community. WDL does not regularly merge commits into the master branch, the main reason for this is we try to avoid pollution of the specification until a set of features has been fully implemented. Once these features have been implemented, we will bump the major or minor version of the spec, raise alot of fanfare and then move on from there.

You can find more about this process outlined in our RFC page : https://github.com/openwdl/wdl/blob/master/RFC.md

Additionally, I would just like to out one pf the active discussion if you would like to contribute: https://github.com/openwdl/wdl/issues/338

- Patrick

[Geet Duggal]

FWIW, from my perspective here at DNAnexus we see a lot of use and interest in WDL in our community of users. There's also a lot of additional open source efforts & collaborations like some of the links above show.  Here's another one to throw into the mix: https://github.com/EliLillyCo/pytest-wdl.  In general, our WDL users enjoy the fact that there is a growing community and that WDL is  developer friendly and easy to read/work with.

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[R.H.P.V...@lumc.nl]

Hello everyone,

The SASC team at Leiden University Medical Center is very invested in WDL. Our manager Leon Mei is promoting interaction with the wider bioinformatics community and encourages us to contribute as much as possible. @DavyCats, @JasperBoom and me (@rhpvorderman) are creating all our new pipelines in WDL in the https://github.com/biowdl group. https://github.com/biowdl/tasks is a resource for reusable WDL tasks that we maintain. We created a intuitive pytest plugin for testing workflows/pipelines here at https://github.com/LUMC/pytest-workflow . It was set up to be as simple as possible to write tests and we test al BioWDL pipelines with it. Having tested pipelines greatly increases our confidence when adding new features or refactoring things.

Also @DavyCats has done great work on a WDL documentation tool: WDL-AID (https://github.com/biowdl/WDL-aid). It can generate inputs pages from WDL files by looking at the parameter_meta section. It depends on miniwdl (thank you @mlin!). For an example of a generated page look here: https://biowdl.github.io/QC/develop/inputs.html .

A former LUMC employee @ffinfo and myself have been making PRs to Cromwell to ensure proper working on HPC clusters. Broad focuses on the cloud, so we made some changes to the SFS backend for our use cases. We have heard from the Prinses Maxima Centrum in Utrecht which uses a similar cluster that they were happy with these changes.

Because of our investment we keep an eye on the OpenWDL github page and contribute to discussions, and sometimes add our own suggestions. We are very happy with WDL as a language, and we hope that the community around it will stay strong. We are very happy with the community contributions which make our life easier everyday. We hope our contributions do the same for others.

Ruben Vorderman

On behalf of the Sequencing Analysis Support Core

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From: Geet Duggal [gdu...@dnanexus.com]
Sent: Wednesday, November 6, 2019 20:20
To: Patrick Magee
Cc: Pieter Lukasse; OpenWDL Community
Subject: Re: WDL or CWL

[Jeff Gentry]

Hi -

Ultimately the decision of whether to use CWL or WDL I think needs to come down to what best suits your needs. In particular consider which engine(s) have which degree of support. Others find that the syntax of one or the other better fits them. That sort of thing.

The reason why there hasn't been much activity on the WDL repo is that the developmental spec got far ahead of known implementations. We have a requirement that any ratified changes are actually implemented by a real world implementation before proceeding, and we're in a holding pattern while implementations catch up.

J