.
├── cluster_logs  # slurm stderr/stdout logs
├── reference
│   ├── reference.chr_lengths.txt  # cut -f1,2 reference.fasta > reference.chr_lengths.txt
│   ├── reference.fasta
│   └── reference.fasta.fai
├── samples
│   └── 
   
      # sample_id regex: r'[A-Za-z0-9_-]+'
│       ├── whatshap/  # phased small variants; merged haplotagged alignments
│       ├── logs/  # per-rule stdout/stderr logs
│       ├── aligned/  # intermediate
│       ├── deepvariant/  # intermediate
│       ├── deepvariant_intermediate/  # intermediate
│       └── whatshap_intermediate/  # intermediate
├── smrtcells
│   ├── done  # move folders from smrtcells/ready to smrtcells/done to prevent re-processing
│   └── ready
│       └── 
    
       # uBAMs or FASTQs per sample
│                        # filename regex: r'm\d{5}[Ue]?_\d{6}_\d{6}).(ccs|hifi_reads).bam' or r'm\d{5}[Ue]?_\d{6}_\d{6}).fastq.gz'
└── workflow  # clone of this repo

    
   

$ conda create \
    --channel bioconda \
    --channel conda-forge \
    --prefix ./conda_env \
    python=3 snakemake mamba lockfile

$ conda activate ./conda_env

$ sbatch workflow/run_snakemake.sh <sample_id>