Data & ReproBioinformatics & GenomicsFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction

bio-workflow-management-snakemake-workflows

Maintainer FreedomIntelligence · Last updated April 1, 2026

Create and manage Snakemake reproducible bioinformatics workflows.

OpenClawNanoClawAnalysisReproductionbio-workflow-management-snakemake-workflows🧠 bioos extended suitebioos extended bioinformatics suitecreate

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-workflow-management-snakemake-workflows

Skill Snapshot

2 min

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

Source Doc

samples:

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

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

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

Use bio-workflow-management-snakemake-workflows for genomics and bioinformatics workflows.
Apply bio-workflow-management-snakemake-workflows to sequencing, variant, or omics analysis tasks.