These are chat archives for chapmanb/obf-codefest

13th
Jul 2017
John Chilton
@jmchilton
Jul 13 2017 19:52
The ideas sheet for the BOSC codefest has what they claim is a link to the workflow for the next DREAM challenge - https://www.synapse.org/#!Synapse:syn8507133/wiki/415976 - but I register and I still don't actually see workflows. Am I incompetent or are they not ready yet?
Denis Yuen
@denis-yuen
Jul 13 2017 19:52
Why not both? (j/k)
The challenge isn't quite ready yet, I think that's the production site
workflows under 3.3
John Chilton
@jmchilton
Jul 13 2017 19:53
True about it being both :D - let me rephrase that - "Is this just another example in a long line of examples of my incompetence or are they not ready yet?"
Great - I requested access ;) - if I have time I'd like to get a running start on doing this for Galaxy for at the codefest if they are not ready in time though I can just fine some simple workflows to test since we don't run any CWL workflows yet :D
Brad Chapman
@chapmanb
Jul 13 2017 19:56
They're not quite ready but almost. Aiming for next week, but most things work (except I broke the bcbio one right before, fixing now). There is a Slack you can ping folks to give you access for testing: https://ga4gh-challenge.slack.com
Denis Yuen
@denis-yuen
Jul 13 2017 19:57
I think a couple of the workflows in the challenge are wdl, but I haven't tried that. But I'm guessing you're looking for a galaxy descriptor (?)
John Chilton
@jmchilton
Jul 13 2017 19:58
No - I want CWL descriptors - I just wanted to use these examples to guide my addition of CWL workflow support to Galaxy
Denis Yuen
@denis-yuen
Jul 13 2017 19:58
Ah cool
Brad Chapman
@chapmanb
Jul 13 2017 20:00
If you want bcbio ones, I have a small self contained test one here: https://github.com/bcbio/test_bcbio_cwl The GA4GH one is a bit bigger and is here: https://github.com/bcbio/bcbio_validation_workflows
John Chilton
@jmchilton
Jul 13 2017 20:21
@chapmanb I like self contained and small - thanks for the link that looks great! I'll open a PR to have Galaxy added to that list by the end of the ISMB :laughing:
Brad Chapman
@chapmanb
Jul 13 2017 20:24
Perfect, I look forward to testing it next week.