Refactor repo structure

For improved reproducibility/reusability, repackage repository according to recommended structure:

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

added To Do label

assigned to @gypas

changed milestone to %First usable version

mentioned in merge request !22 (merged)

closed via merge request !22 (merged)

mentioned in commit fdc358f4