Update repo structure following best practices

[supermaxiste]

Since some time, the Snakemake team set best practices to set up a repository with a Snakemake workflow. The main change to apply would be to follow a standardized structure for the repository:

├── .gitignore
├── README.md
├── LICENSE.md
├── workflow
│   ├── rules
|   │   ├── module1.smk
|   │   └── module2.smk
│   ├── envs
|   │   ├── tool1.yaml
|   │   └── tool2.yaml
│   ├── scripts
|   │   ├── script1.py
|   │   └── script2.R
│   ├── notebooks
|   │   ├── notebook1.py.ipynb
|   │   └── notebook2.r.ipynb
│   ├── report
|   │   ├── plot1.rst
|   │   └── plot2.rst
|   └── Snakefile
├── config
│   ├── config.yaml
│   └── some-sheet.tsv
├── results
└── resources