Benefits:

• separates workflow logic from data
• easier debugging
• easier collaboration

Common practice:

• config -> parameters and sample tables
• envs -> reproducible environments
• rules -> modular workflow steps
• results -> generated outputs

A clean directory structure makes pipelines easier to maintain and reproduce.

Snakefile Breakdown

• Fastq files that need trimming - input: sample.fastq
• Cutadapt - output: sample-trimmed.fastq
• BWA - align trimmed fastq to assembly output: sample-aligned.sam
• Samtools sorting, indexing - output: sample-sorted.bam
• Freebayes variant calling - output: sample-variants.vcf

Example snakefile

rule all:
    input:
        "variants/sample1.vcf"

rule trim:
    input:
        "reads/sample1.fastq"
    output:
        "trimmed_reads/sample1-trimmed.fastq"
    shell:
        "cutadapt -A TCCGGGTS -o {output} {input}"

rule align:
    input:
        "trimmed_reads/sample1-trimmed.fastq"
    output:
        "bam/sample1.bam"
    threads: 1
    shell:
        "bwa mem -t {threads} ref.fa {input} | samtools view -Sb - > {output}"

Snakemake takes the first rule as the target, then constructs a graph of dependencies.

Wildcards serve as placeholders within rules to operate on multiple files via pattern matching.