Integrate whatever we feel is useful from the nf-core template

[madeline-scyphers]

nf-core when creating a new pipeline (https://nf-co.re/docs/nf-core-tools/pipelines/create), even if using nf-core resources outside of nf-core (https://nf-co.re/docs/guidelines/external_use) comes with a bunch of useful stuff. Like really great configuration splitting and defaults/overriding, setting up a bunch of profiles, setting of NF testing and NF CI, NF linting, NF email and slack support, and a bunch more. It would be great to utilize this to get the NF repo part into better shape.

[madeline-scyphers]

Maybe easier to do if we do #366 first since then we could also use their containerization from biocontainers or seqera containers stuff.