Workflows

bsaseq ships Nextflow and Snakemake templates in workflows/ for scalable, reproducible runs on HPC.

Nextflow

nextflow run workflows/nextflow/main.nf \
    --vcf /path/to/variants.vcf.gz \
    --high_bulk "mut1,mut2" \
    --low_bulk "wt1,wt2" \
    --outdir results

Requires Nextflow >= 23.04 and one of Docker, Singularity/Apptainer, or Conda.

Snakemake

cp workflows/snakemake/config.yaml my_analysis.yaml
# edit my_analysis.yaml (vcf, high_bulk, low_bulk, ...)
snakemake --configfile my_analysis.yaml --cores 1 --use-conda

Requires Snakemake >= 7.0. See the READMEs in each workflow directory for the full parameter list.