feat: Add support for Nix Flakes through nix develop

[GuilloteauQ]

Description

Add support for Nix Flakes.

Before, when users wanted to use Nix Flakes (https://nixos.org) they had to wrap the shell command into the cli call to nix develop:

shell:
    "nix develop .#myenv --command 'python3 run.py'"

with this PR, users can indicate which Nix environment to use, similarly to containers and conda:

nix_flake:
    ".#myenv"
shell:
    "python3 run.py"

Related issue: #139

QC

• The PR contains a test case for the changes or the changes are already covered by an existing test case.
• The documentation (docs/) is updated to reflect the changes or this is not necessary (e.g. if the change does neither modify the language nor the behavior or functionalities of Snakemake).

This PR adds a simple test for the feature.
I am unsure how to add it to the test suite though because of the Nix dependency....

For the doc, I will be happy to write a section if this PR gets accepted :)

[sonarcloud]

Kudos, SonarCloud Quality Gate passed!   

0 Bugs
0 Vulnerabilities
0 Security Hotspots
0 Code Smells

No Coverage information
0.0% Duplication

[johanneskoester]

This is awesome, thanks a lot! Please be patient with me, we are currently preparing for Snakemake 8 which will support all kinds of plugins. So far, I am working on storage and executor plugins, but deployment plugins are also on my list. I still have to decide whether I merge this as is or whether we rather immediately do this as a plugin, which you could then even maintain directly yourself.