snakemake

Snakemake: Workflow Management

Overview

Snakemake is a workflow management system that allows you to create reproducible and scalable data analysis pipelines. It is widely used in bioinformatics for automating computational biology workflows.

When to Use This Skill

This skill should be used when:

• Creating automated analysis pipelines
• Ensuring reproducibility
• Scaling workflows to clusters/cloud
• Managing complex dependencies
• Building single-cell analysis pipelines

Quick Start

Installation

# Using conda
conda install -c conda-forge snakemake

# Using pip
pip install snakemake

Basic Workflow

# snakefile
rule all:
    input:
        "results/aligned.bam"

rule align:
    input:
        "data/sample.fastq"
    output:
        "results/aligned.bam"
    shell:
        "bwa mem {input} > {output}"

Single-Cell Example

Complete scRNA-seq Pipeline

# snakefile
configfile: "config.yaml"

rule all:
    input:
        expand("results/{sample}/qc_report.html", sample=config["samples"])

rule qc:
    input:
        "data/{sample}.fastq.gz"
    output:
        html="results/{sample}/qc_report.html",
        json="results/{sample}/qc_metrics.json"
    shell:
        """
        fastqc {input} -o results/{wildcards.sample}/
        multiqc results/{wildcards.sample}/ -o {output.html}
        """

rule trimming:
    input:
        "data/{sample}.fastq.gz"
    output:
        "results/{sample}/trimmed.fastq.gz"
    shell:
        "trim_galore {input} -o results/{wildcards.sample}/"

rule alignment:
    input:
        "results/{sample}/trimmed.fastq.gz"
    output:
        "results/{sample}/aligned.bam"
    shell:
        "star --genomeDir {config[genome]} --readFilesIn {input} --outFileNamePrefix results/{wildcards.sample}/"

rule count:
    input:
        "results/{sample}/aligned.bam"
    output:
        "results/{sample}/counts.txt"
    shell:
        "featureCounts -a {config[gtf]} -o {output} {input}"