I think this particular conditional could be flattened by moving the unvalidated one into the main select, then checking whether or not the custom flag is needed in cheetah
The next workflows call is in 60 minutes:
Workflow WG call
Thursday, 17 November · 16:00 – 17:00
Google Meet joining info
Video call link: https://meet.google.com/myu-vozy-bsj
Workflow WG call
Thursday, 17 November · 16:00 – 17:00
Google Meet joining info
Video call link: https://meet.google.com/myu-vozy-bsj
Sounds like there's some movement on the workflowhub side, but will do!
I think I got most of the backend modalities worked out for conditional steps, if you want to have a look at the test case and assumptions, they're in lib/galaxy_test/api/test_workflows.py here: https://github.com/galaxyproject/galaxy/pull/14846/files#diff-62218e13fbfad227cca222eb36d1801285ceb01eb2f9eb0c14aa99175bddd762R1896 ... no UI yet, that's the next thing I'll work on
Thanks
Just for information, this could be part of 23.0? Is that the idea?
Guess we got ~ 2-3 weeks to get the user interface in, it seems doable if there's no too many unexpected things popping up
I tried this morning, but we have to wait for the bioconductor rebuild to finish
otherwise we may not have all dependencies on usegalaxy.org
what is the rule for subworkflows in the iwc repo? should i have a separate folder with tests or is it enought that they are tested in the main workflows ?
If they're useful on their own it certainly is easier for you to have separate tests, yeah
What can/should be done about tool versions used in a workflow that are missing on usegalaxy.org? If someone tells me I would add it here: https://github.com/galaxyproject/iwc/blob/main/workflows/README.md#optional-updating-tools :)
(its the newest version of the NCBI dataset download tool)
that's here: https://github.com/galaxyproject/usegalaxy-tools#requesting-a-new-tool-or-updating-a-tool ... but don't add it, we'll automate this, that's just extra cognitive load
(also we should be able to install tools as well during tests)
awesome
that would have been a strange error to have otherwise
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Hi all -- is this even possible? Guessing the workflow invocation view needs to access the server's existing HTML "allow-list". https://help.galaxyproject.org/t/how-to-display-multiqc-report-in-workflow-invocation-report/9115
I'm testing this out at ORG in a fresh history. Maybe they are working at a local server and just need to add the tool to their allowlist
I had misunderstood what they wanted (maybe). From "User > Workflow invocations" the outputs are listed out and drilling down to HTML output is rendered correctly. BUT I think what they want is to add in are output datasets to the "Report" function. No other outputs are fully rendered -- the report just has the workflow/tool parameters, and I think that is fine. I'll write them back with the how-to for all cases.
I guess it is an issue with the delta which is too low.
I guess it would be helpful to know what the delta that we get in the test actually is 🤔
I'm using this
cut tool in a workflow (on 22.01) .. the workflow has then always extra chars in the field selector, i.e. the command line is cut -f '1__cn__'... which fails. Is there a trick to this?
we've backported this pretty far, so it should work on the head of 22.01
cut1 doesn't use the data_column, so be careful that there's no newline in the editor field
I suppose we should strip this in the tool itself ?