Instead of defining steps , you define rules that produce files .

rule align:

input:

“reads.fastq”

output:

“aligned.bam”

shell:

“bwa mem ref.fa {input} > {output}”

Snakemake builds a directed acyclic graph (DAG) automatically.

Fastq → Cutadapt → BWA → Sorted BAM → Freebayes → VCF