Hey there,
I’m on - usegalaxy.eu
here is the workflow invocation - Galaxy
History - Galaxy
The Workflow always fails to schedule jobs at exactly this step when running it with this configuration!
Hello @Smkingsize
Thank you for sharing all the details/links. Very helpful!!
I clicked into the Steps tab to review the completed/pending jobs, and it looks like one of the subworkflows inside the master workflow was not also set to a shared state?
You could ask the owner to share all of the parts of this workflow again. Then you could try the workflow rerun button to duplicate the prior run. (I’m not sure if a resume is enough for this use case .. but you could also try that to test it).
If that is not enough, would you please explain a bit more about where this was sourced? I checked Public Workflows at the EU server and didn’t find this but could have missed it from a different public source.
Let’s start there, thanks! 
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Hey thanks for your reply!
so the Sub-workflow is also made by me. and I just checked and tried to reconnect it but still the scheduler fails. and the wired thing is that the sub workflow actually runs successfully (screen shot from step 24. innvocation - Galaxy):
it’s just that the jobs afterwards are not being scheduled and I am using the sub workflow twice. the first 1 passes just fine but it always stoops scheduling after the 2nd one!
thank you
@Smkingsize I’m not sure whether this is really causing the problem, but you are cheating with the conditional inputs leading up to the failing sub-workflow invocation.
Can you please follow what I described here: Optional steps in workflow can't be connected to one another , i.e. use Pick param steps to get rid of the orange connections?
Thanks for the hint. yes indeed I was cheating with the optional parameters connections 
However I’ve used the work around and got rid of all the orange connection but the problem is still present 
here is the last invocation: Galaxy
That was some nasty debugging
Turns out the error has nothing to do with the sub-workflows. Instead you’re defining the optional “Reference” input (number 4) to be a list and define all processing in the “Genome Reconstruction” part to work with lists. This is also true for steps 30 and 31 in “Best Organism”.
However, when “Reference” is not provided, all these steps operate on the output of the “Hybrid Assembly” part, which is a single dataset. Surprisingly this doesn’t cause an issue up to step 32, which is an “Extract Dataset” step. This one needs list input and cannot be scheduled on a single dataset.
So you have to decide: either both branches of your WF need to process collections or single datasets.
Small remark: There’s also a disconnected Step 6: Pick parameter value in the current version.
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This explains a lot 
I’ve did as you said it and it did actually fix the issue.
Thanks a lot! I’ve also benefited from the optional parameters tip.
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