there's a bunch of different possible causes, like filtered out outputs or bugs
fwiw, maybe it's related, but whenever I open the workflow in the editor, it always tries to delete the final connection (to the problematic output) if I try and modify the tool
anyway, I was planning to make an IWC PR, so I will push it there
I can also try and create a more minimal case
it seems it isn't possible to add citations to a workflow, as it is for tools?
would be a useful feature imo
I'm prepping to look into the minimal workflow you posted Simon Bray , one thing I noticed is that gmx_sim isn't at the latest version. Might be totally unrelated of course
arg, I can't read, I just didn't install the right version it looks like
<collection name="outp_col" type="list" label="Free energy data">
<discover_datasets pattern="(?P<designation>^cluster\d+)_outp\.txt$" ext="tabular"/>
<filter>
json
</filter>
</collection>
<collection name="outp_frict_col" type="list" label="Friction data">
<discover_datasets pattern="(?P<designation>^cluster\d+)_ofrict\.txt$" ext="tabular"/>
<filter>
json
</filter>
</collection>
<data name="outp" from_work_dir="outp.txt" format="tabular" label="Free energy data">
<filter>
not json
</filter>
</data>
<data name="outp_frict" from_work_dir="ofrict.txt" format="tabular" label="Friction data">
<filter>
not json
</filter>
</data>that seems to be the problem, the workflow defines a workflow output outp_col, but it seems that output is being filtered out because there's no input connected to Ensemble subgroups (the json parameter). Does that make sense ? I think this might be one of the cases where the workflow editor cannot accurately predict the result of the filter
Since otherwise you'd expect to have labelled
outp, correct ?
Thanks for having a look Marius!
I will test it tomorrow on the real workflow, but I'm sure that's it
Could I have a review of galaxyproject/iwc#68, when someone has time, from a technical, IWC point of view?
Chris Barnett agreed to review it from the scientific side
If you want to get the tests passing you could take a look into either installing the tools on usegalaxy.org via https://github.com/galaxyproject/usegalaxy-tools or seeing if we can remove
--no_shed_install from https://github.com/galaxyproject/planemo-ci-action/blob/main/planemo_ci_actions.sh#L6
hm, in the latter case you would switch to testing on a local galaxy, not on usegalaxy.org, right?
just the tools and reference data come from cvmfs
so you don't have to reinstall the tools each time
exactly ... although it also takes a long time to start up, if we load all the tools that we don't actually use, maybe we'd be better off to just have the reference data on cvmfs
and test against live servers as separate jobs
Do we have anything for generating RO Crates from workflows? I've had a quick google and found nothing
but the WorkflowHub people finally seem to have an API so maybe we can do that in the GTN
that might be just the ticket, thanks wm75 (Wolfgang Maier)
oh and built in upload to WFH? fab
ok, yeah that might be it
yes, but please push them towards a github app. this is just insane that we have to do this
we would like to publish a paper referring to these workflows by the end of December, and it would be ideal if they were in the IWC by then
Nope, but no idea why the tests didn't run
Thanks a lot! Do you have any comment here: https://github.com/galaxyproject/iwc/pull/68#discussion_r757525658
Hmm, I don't think that's too bad ... it's not that different from downloading accessions from the sra for instance. I guess it would be cool if we could have an optional data input with a default that fetches the file