Provide execution engines via the nexflow.config

[hoelzer]

Hey,

I see that you have different profiles for the dependency handling (conda, docker, ...) but in my experience its also more convenient to provide some basic execution profiles such as local, slurm, lsf, ...

This is way easier than letting the user inject any additional config or modify the .bashrc etc...

Here is an example:

https://github.com/hoelzer/pocp/blob/main/nextflow.config#L49-L68

Then the user can simply merge dependency profiles and execution profiles, e.g.

nextflow run rki-mf1/GARI -r 0.0.1 -profile local,docker
nextflow run rki-mf1/GARI -r 0.0.1 -profile slurm,mamba
nextflow run rki-mf1/GARI -r 0.0.1 -profile slurm,singularity

etc.

I also suggest adding information about the available profile options to the --help

https://github.com/hoelzer/pocp/blob/main/main.nf#L219-L232

(of course these are just examples, pls feel free to adapt)