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Snakemake for Bioinformatics

Snakemake for Bioinformatics
Key Points
Glossary
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Snakemake for Bioinformatics

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EPISODES

Summary and Setup

1. Running commands with Snakemake

2. Placeholders and wildcards

3. Chaining rules

4. Complex outputs, logs and errors

5. How Snakemake plans its jobs

6. Processing lists of inputs

7. Handling awkward programs

8. Finishing the basic workflow

9. Configuring workflows

10. Optimising workflow performance

11. Conda integration

12. Constructing a whole new workflow

13. Cleaning up

Key Points
Glossary
Learner Profiles
Extra Episode: Robust quoting in Snakefiles
Discussion
Prerequisites
Reference

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Discussion

Last updated on 2024-02-22 | Edit this page

For active discussions, see the open issues in GitHub.

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Materials licensed under CC-BY 4.0 by the authors

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