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

Snakemake take first rule as target then constructs graph of dependencies

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}"

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