Home Documentation

Presentations

• http://slides.com/johanneskoester/deck-1#

Tutorials

• https://github.com/leipzig/SandwichesWithSnakemake
• Snakemake Tutorial
• https://slowkow.com/notes/snakemake-tutorial/

Examples

• inodb/snakemake-workflows (NGS - metagenomics)
• daler/enhancer-snakemake-demo

Papers

• Snakemake—a scalable bioinformatics workflow engine
• Parallelization, Scalability, and Reproducibility in Next-Generation Sequencing Analysis

Resources

• snakemake-rules
• Snakemake Workflow Repository
• Snakemake Wrapper Repository

Discussion

• https://www.biostars.org/p/88277/

Illustrate

• embedded Python
• wrappers
• benchmarks
• reports
• dag
• expand
• config
• input functions
• rule params
• logging
• temporary/protected files