README.md.jinja

# snakemake-workflow-ref_genomes ({{ species.replace("_", " ").upper() }})

A Snakemake workflow to download various files from Ensembl for a given reference genome and create a STAR aligner index.

**Creation Date:** {{ date }}
**Species:** {{ species.replace("_", " ").upper() }}

## Getting Started

```shell
mkdir /media/user/data/genomes
docker volume create --opt type=none --opt o=bind --opt device=/media/user/data/genomes genomes

mkdir /media/user/data/conda-envs
docker volume create --opt type=none --opt o=bind --opt device=/media/user/data/conda-envs conda-envs

# Build the workflow image
docker compose build workflow

# Run Snakemake within the workflow service to automatically run the workflow
docker compose run --rm -it workflow snakemake --use-conda -c2 -p -n

# The rules that would be run if it wasn't in dry mode should show up
# If everything looks, good, remove the -n flag and run it for real...
docker compose run --rm -it workflow snakemake --use-conda -c2 -p 
```