.
├── cluster_logs # slurm stderr/stdout logs
├── config.yaml # customized copy of example_config.yaml
├── output_trio_assembly # output directory
│ └── <trio_id>
│ ├── fasta
│ ├── hifiasm
│ ├── logs
│ └── yak
└── workflow_trio_assembly # clone of this repo ├── calN50 └── rules └── envs

# clone workflow from github into directory named `workflow_trio_assembly`
git clone --recursive [email protected]:juniper-lake/trio-assembly-snakemake.git workflow_trio_assembly
# create directory for cluster logs to be stored.
mkdir cluster_logs
# create `config.yaml` based on `example_config.yaml`.
cp workflow_trio_assembly/example_config.yaml config.yaml
# adjust paths in Snakefile and sbatch script as necessary
# create conda environment to run snakemake workflow.
conda create --prefix ./conda_env --channel bioconda --channel conda-forge lockfile==0.12.2 python=3 snakemake mamba
# activate conda environment. **This conda env must be activated each time you run the workflow.**
conda activate ./conda_env
# run workflow by submitting sbatch script with <trio_id>.
sbatch workflow_trio_assembly/run_snakemake.sh <trio_id>