Pipeline needs updating to the latest template version

[ewels]

The pipeline is now getting a bit behind the nf-core template. It needs to be updated before any further development work can be done on the pipeline.

First, the TEMPLATE branch needs to be fixed - #13

Then a new automated sync PR needs to be created, as fixing #13 will remove the commits in #12 (closing new preemptively).

Again, I will try to have a go at fixing this stuff up myself in the coming days. At least opening the PR anyway, I will see about resolving the merge conflicts. If they're not too bad then I will try.