Added new workflow to polish assembly

[AnnaSyme]

Added to folder "genome-assembly", in subfolder "polish-with-long-reads"

[AnnaSyme]

ping @mvdbeek this is ready to go if you wouldn't mind having a look?

[mvdbeek]

Looks great, my only suggestion is to restrict the minimap profile parameter values that the user can select (or provide a list of options, if some of them don't make sense)

[AnnaSyme]

thanks @mvdbeek this is a good idea. I want to provide a default value but also a list of suggested values. However is this possible? When I do put in the default, but also the suggested values, I can't see them in the drop-down list when I go to run the workflow. If I have no default value, I can see all the suggested values. Is there a way around this?

[mvdbeek]

Kind of, the default value only works for optional parameters, so what would work (but is a little clunky) is when you define the possible parameters, you can put the default first.

[AnnaSyme]

thanks have done this for these suggested values @mvdbeek

[mvdbeek]

Do you need to move Galaxy-Workflow-Assembly_polishing_with_long_reads.ga to Assembly_polishing_with_long_reads.ga ? There are now two workflows in here, and only one has a test.

[AnnaSyme]

Thanks @mvdbeek - I've removed the older workflow and re-named the newer one - does that look ok?

[mvdbeek]

very cool, I'll merge when the tests are passing!

[bgruening]

🎉 🎉 🎉 🎉 🎉 🎉