SnakeMake best practices

[reid-a]

SnakeMake best practices

[ocaisa]

This looks more promising for our use case https://github.com/jdblischak/smk-simple-slurm

[reid-a]

Related: SnakeMake also comes with a linter, and there are more general best practices in the documentation, which we should review and follow to the degree they make sense.

[ocaisa]

Regarding the use of profiles, this is a bit of a rabbit hole as to get snakemake to query the status of jobs you need a complex setup. This is solved by using cookie cutter profiles (as suggested by @vinisalazar) but that's a complex topic to teach so early in the lesson. It also impacts our portability a bit, since obviously we'll need different profiles for different schedulers.

A good example of why you want this is at snakemake/snakemake#1164

[ocaisa]

See https://github.com/Snakemake-Profiles/slurm for the Slurm profile

[bkmgit]

Profiles are helpful to avoid typing -c 1 at every invocation. Is Slurm something to emphasize throughout the lesson or enable flexible use both locally and on remote machines? One can also use Terraform to use cloud resources.