How would you prefer to access the GATK doc JSONs?

[vdauwera]

Hi, I’m responsible for GATK docs and just came across this project; it seems like a really useful thing for GATK users and we’d like to support it as much as we can. Full disclosure, we’re working on something similar for WDL.

It looks like you’re scraping the website for the JSONs, and I think that’s something we can help improve most immediately. I can think of a few options; for example we could make a zip file available per version, or we could include them in the GATK github repo. What would you find most convenient? Feel free to suggest other mechanisms.

Down the road we may even be able to host the generated CWLs, if you’re interested in working with us on that.

Feel free to email me directly at Geraldine@broadinstitute.org to discuss.

[mr-c]

Hello @vdauwera !
Either works. Right now the website has changed so much that this tool is broken. Where can I find the JSON files today?

[vdauwera]

Ah, sorry about that, @mr-c! I'm checking with the team -- we had discussed posting a zip file somewhere or checking the JSONs into the GATK repo itself (as noted in my comment), but I'm not sure what ended up happening as I'm no longer as closely involved in those decisions. Will try to find out.

[mr-c]

Thanks. I was able to work around by downloading https://github.com/broadinstitute/gatk/releases/download/4.1.6.0/gatk-4.1.6.0.zip, self-hosting the gatkdocs directory, and pointing this tool to http://localhost/... :-D

[vdauwera]

Hah ok! Nevertheless, I think we can provide something a little simpler -- I just had a quick slack chat with the engine team and they're going to look at the feasibility of adding a zip file of the JSONs as a release asset in github. Would that work? It should make it possible to fetch them per release with an API call to github iirc.

Incidentally, they've also been building in some capabilities to autogenerate WDL wrappers. I wonder if that might be helpful to you?

[mr-c]

That sounds feasible! gatk-cwl-generator is not my project, I'm just a user. That said, I would not be sad if you all shipped official CWL tool descriptions with future releases.

[vdauwera]

That would make me happy too, tbh -- but it might be a hard sell for the engine team. I make no promises…