├── Snakefile├── config/│ └── config.yml├── envs/│ └── bwa.yml├── rules/│ ├── alignment.smk│ ├── qc.smk│ └── variant_calling.smk├── scripts/│ └── custom_processing.py├── data/│ └── raw/├── results/│ ├── bam/│ ├── qc/│ └── variants/└── logs/

Can also create a environment.yml file, list conda envs and what to install

name : bwa.yml

channels:

- conda-forge

• bioconda

dependencies :

-bwa= 0.7.17

.yml file can indicate how to make conda environment and what packages and dependencies you need