Snakemake

Snakemake uses a readable, Python-based rule syntax inspired by GNU Make. It automatically determines dependencies and only re-runs what changed.

Example

1rule align:
2    input: "reads/{sample}.fq"
3    output: "aln/{sample}.bam"
4    threads: 8
5    shell: "minimap2 -ax map-ont ref.fa {input} | samtools sort -o {output}"
Copy

Integrates with conda/containers and the Snakemake Workflow Catalog.