bio-workflow-management-snakemake-workflows

Version Compatibility

Reference examples tested with: BWA 0.7.17+, FastQC 0.12+, MultiQC 1.21+, Nextflow 23.10+, Salmon 1.10+, Snakemake 8.0+, bcftools 1.19+, fastp 0.23+, pandas 2.2+, samtools 1.19+, scanpy 1.10+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures
• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Snakemake Workflows

"Build a reproducible bioinformatics pipeline with Snakemake" → Define analysis steps as rules with input/output declarations, automatic dependency resolution via wildcards, and cluster execution support for HPC/cloud environments.

• Python: Snakefile rule syntax with expand(), wildcards, and config for parameterization

Compatible with Snakemake 7.x, 8.x, and 9.x. For Snakemake 8.0+, use --executor instead of --cluster.

Basic Rule Structure

# Snakefile

rule all:
    input:
        expand("results/{sample}_counts.txt", sample=SAMPLES)

rule align:
    input:
        r1 = "data/{sample}_R1.fq.gz",
        r2 = "data/{sample}_R2.fq.gz",
        index = "ref/genome.fa"
    output:
        bam = "aligned/{sample}.bam"
    threads: 8
    shell:
        "bwa mem -t {threads} {input.index} {input.r1} {input.r2} | "
        "samtools sort -@ {threads} -o {output.bam}"

Config File

# config.yaml
samples:
  - sample1
  - sample2
  - sample3

reference: "ref/genome.fa"
threads: 8

# Snakefile
configfile: "config.yaml"

SAMPLES = config["samples"]
REF = config["reference"]

rule all:
    input:
        expand("results/{sample}.bam", sample=SAMPLES)

Wildcards and Expand

# Define samples
SAMPLES = ["A", "B", "C"]
CHROMOSOMES = [str(i) for i in range(1, 23)] + ["X", "Y"]

# Expand for all combinations
rule all:
    input:
        expand("results/{sample}_{chrom}.vcf", sample=SAMPLES, chrom=CHROMOSOMES)

# Access wildcard in rule
rule process:
    input:
        "data/{sample}.bam"
    output:
        "results/{sample}.vcf"
    params:
        sample = lambda wildcards: wildcards.sample
    shell:
        "bcftools call -s {params.sample} {input} > {output}"