implement snaketool build fixes

[beardymcjohnface]

per title, implement the recent build fixes documentation that were pushed to snaketool

[cpauvert]

Hi @beardymcjohnface
Thanks for providing such a cookiecutter! I'm currently playing around with a nextflow workflow I wan to turn into an app using Nektool.
How much of the fixes in Snaketool are lacking in Nektool? Do you have an estimated timeline for fixes, or list the commits in Snaketool, to flag them for others to implement?
Best,