Adapt assembly workflows to work on Toil

[adamnovak]

This PR contains changes I needed to make to get the assembly workflows working with Toil as the WDL runner. There's going to be another PR of the corresponding changes to Toil to fix Toil bugs that the workflows trigger, but this I think fixes some workflow bugs.

• sep isn't actually allowed in placeholders outside of commands in WDL 1.0, and isn't properly implemented there by Cromwell anyway, so change to checking array length
• If attempts to delete the input files provided to a step fail, ignore the failure and leave the input files in place. They can't be deleted in MiniWDL or Toil without making extra copies expressly for that purpose.
• We can't multiply by homCov if it isn't set, so we need to do something to make that typecheck. I actually ran it by making homCov required, but now I see there are run types when you may not actually want to provide it. So now I added a select_first call and am testing to make sure that still works.

[adamnovak]

I tested the final version of this and it works!