The only rather stupid-looking solution I have is to extract, as part of a workflow, each multi-sequence fasta (it's always eight of them) with
__EXTRACT_DATASET__, then run vapor on each of those datasets and the list:paired collection.
I can live with that if it's the only way, but don't want to build something dumb.
So instead of lining up collections to be processed match by match you want to do all possible combinations?
IIRC we do support that in the backend, but haven't enabled this for lack of a user interface. Just to be sure, can you share a history with your workaround ? I wonder if this could also be done by nesting your collection deeper
https://usegalaxy.eu/u/wolfgang-maier/h/vapor-nested-attempts
Collections 11 and 15 are the relevant inputs.
Collections 11 and 15 are the relevant inputs.
hey workflow gurus! staramr specifies species using a drop down (this is necessary to run PointFinder) - while the user could set this by changing the "default tool parameters" at pipeline invocation time, is there any way to ask for a user input parameter for the pipeline (so it shows up right at the top like other pipeline inputs) and connect this to the dropdown?
Yes, you can click on the
add connection to module button, then connect a text parameter to that input
It'll be shown as a select list
Note that only works for selects, not conditionals, since conditionals can add arbitrary inputs and outputs, breaking workflows
ah damn, the staramr input is a conditional - instead of making it "use pointfinder: yes / no" and then "which database", they (PHAC-NML) combined it into one
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