rule bwa_map:
input:
"data/genome.fa",
"data/samples/{sample}.fastq"
output:
"mapped_reads/{sample}.bam"
shell:
"bwa mem {input} | samtools view -Sb - > {output}"

With the above `Snakefile` in the current directory, if you run `snakemake -np mapped_reads/B.bam` it matches the output, `mapped_reads/B.bam` with the matching output, and decides that the value of `{sample}` is `B`, and looks at the input dependencies, and if they have changed, runs the `shell` script.

rule plot_quals:
input:
"calls/all.vcf"
output:
"plots/quals.svg"
script:
"scripts/plot-quals.py"

The `script` will be evalauted relative to the `Snakemake` file. The script will have access to a global variable `snakemake`, which contains `.input` and `.output` (`string lists`) representing the input and output files matching the rule.