snakemake

name	snakemake
description	Snakemake — Python-based workflow management for reproducible bioinformatics (rules, conda/container integration, cluster execution). Use when encoding shotgun metagenomics DAGs as Snakefiles or adopting community metagenomics snakemake pipelines. Upstream: https://github.com/snakemake/snakemake. Route via research-analysis / metagenomics-workflow / setup. Alternative: nextflow.
license	MIT
category	utilities
tags	["Snakemake","workflow","reproducibility","pipeline","conda","HPC"]
upstream	https://github.com/snakemake/snakemake
stage	utilities

Snakemake

Upstream: snakemake/snakemake · Docs: https://snakemake.readthedocs.io/

Citation

Mölder, F. et al. Sustainable data analysis with Snakemake. F1000Res. 10, 33 (2021). https://doi.org/10.12688/f1000research.29032.2

Original: Köster, J. & Rahmann, S. Snakemake—a scalable bioinformatics workflow engine. Bioinformatics 28, 2520–2522 (2012). https://doi.org/10.1093/bioinformatics/bts480

See also docs/references.md.

Analytical thinking

Snakemake maps well to rule-based metagenomics DAGs (QC → assembly → … → multiqc / tables for research-analysis). Use conda/mamba or containers per rule; pin Snakemake major version and environment YAML hashes. Prefer dry-run (-n) before cluster submit.

How to run

# conda install -c bioconda snakemake
snakemake -j 16 --use-conda
# or: snakemake -j 100 --cluster 'sbatch ...' --latency-wait 60

Decision tree

Workflow manager?
├─ Snakemake / conda-centric → snakemake
├─ Nextflow / nf-core → nextflow
└─ Manual stages → metagenomics-workflow + setup

Related skills

nextflow · setup · metagenomics-workflow · research-analysis · tool-selection · multiqc