feat!: Update snakemake to v8

[tedil]

This PR updates snakemake to version 8.

ToDo

• adapt to snakemake API changes
• use modules instead of subworkflows
• update environment yaml and requirements files
• merge requirements files into environment.yaml as much as possible
• use slurm executor plugin instead of custom job submission scripts

Miscellaneous

• renames all rule alls to rule ${WORKFLOW}_all and sets default_target: True for those. In principle, we could simply get rid of the ${WORKFLOW} prefix for all rules, since the module system allows specifying a custom prefix.

[github-actions]

• Please format your Python code with ruff: make fmt
• Please check your Python code with ruff: make check
• Please format your Snakemake code with snakefmt: make snakefmt

You can trigger all lints locally by running make lint

[coveralls]

coverage: 85.772% (+0.002%) from 85.77%
when pulling ee4cbe1 on snake8
into 0d03919 on main.