https://github.com/snakemake/snakemake-workflow-catalog
A statically generated catalog of available Snakemake workflows
https://github.com/snakemake/snakemake-workflow-catalog
Last synced: 9 days ago
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A statically generated catalog of available Snakemake workflows
- Host: GitHub
- URL: https://github.com/snakemake/snakemake-workflow-catalog
- Owner: snakemake
- License: mit
- Created: 2020-12-26T22:25:08.000Z (over 5 years ago)
- Default Branch: main
- Last Pushed: 2024-06-28T22:54:34.000Z (about 2 years ago)
- Last Synced: 2024-06-29T00:15:36.672Z (about 2 years ago)
- Language: HTML
- Homepage: https://snakemake.github.io/snakemake-workflow-catalog
- Size: 313 MB
- Stars: 28
- Watchers: 6
- Forks: 10
- Open Issues: 5
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# snakemake-workflow-catalog
[](https://github.com/snakemake/snakemake-workflow-catalog/actions/workflows/generate.yml)
[](https://github.com/snakemake/snakemake-workflow-catalog/actions/workflows/pages/pages-build-deployment)
A statically generated catalog of available Snakemake workflows
This repository serves as a centralized collection of workflows designed to facilitate reproducible and scalable data analyses using the [**Snakemake**](https://snakemake.github.io/) workflow management system.
## Purpose
The Snakemake Workflow Catalog aims to provide a regularly updated list of high-quality workflows that can be easily reused and adapted for various data analysis tasks. By leveraging the power of [**Snakemake**](https://snakemake.github.io/), these workflows promote:
- Reproducibility: Snakemake workflows produce consistent results, making it easier to share and validate scientific findings.
- Scalability: Snakemake workflows can be executed on various computing environments, from local machines to high-performance computing clusters and cloud services.
- Modularity: Snakemake workflows are structured to allow easy customization and extension, enabling users to adapt them to their specific needs.
## Workflows
Workflows are automatically added to the Workflow Catalog. This is done by regularly searching Github repositories for matching workflow structures. The catalog includes workflows based on the following criteria.
### All workflows
- The workflow is contained in a public Github repository.
- The repository has a `README.md` file, containing the words "snakemake" and "workflow" (case insensitive).
- The repository contains a workflow definition named either `Snakefile` or `workflow/Snakefile`.
- If the repository contains a folder `rules` or `workflow/rules`, that folder must at least contain one file ending on `.smk`.
- The repository is small enough to be cloned into a [Github Actions](https://docs.github.com/en/actions/about-github-actions/understanding-github-actions) job (very large files should be handled via [Git LFS](https://docs.github.com/en/repositories/working-with-files/managing-large-files), so that they can be stripped out during cloning).
- The repository is not blacklisted here.
### Standardized usage workflows
In order to additionally appear in the "standardized usage" area, repositories additionally have to:
- have their main workflow definition named `workflow/Snakefile` (unlike for plain inclusion (see above), which also allows just `Snakefile` in the root of the repository),
- provide configuration instructions under `config/README.md`
- contain a `YAML` file `.snakemake-workflow-catalog.yml` in their root directory, which configures the usage instructions displayed by this workflow catalog.
Typical content of the `.snakemake-workflow-catalog.yml` file:
```bash
usage:
mandatory-flags: # optional definition of additional flags
desc: # describe your flags here in a few sentences (they will be inserted below the example commands)
flags: # put your flags here
software-stack-deployment: # definition of software deployment method (at least one of conda, singularity, or singularity+conda)
conda: true # whether pipeline works with --use-conda
singularity: true # whether pipeline works with --use-singularity
singularity+conda: true # whether pipeline works with --use-singularity --use-conda
report: true # add this to confirm that the workflow allows to use 'snakemake --report report.zip' to generate a report containing all results and explanations
```
Once included in the standardized usage area you can link directly to the usage instructions for your repository via the URL `https://snakemake.github.io/snakemake-workflow-catalog?usage=/`.
### Release handling
If your workflow provides Github releases, the catalog will always just scrape the latest non-preview release. Hence, in order to update your workflow's records here, you need to release a new version on Github.
## Contributing
Contributions to the Snakemake Workflow Catalog are welcome!
Ideas can be discussed on the [catalog's Issues page](https://github.com/snakemake/snakemake-workflow-catalog/issues) first, and contributions made through Github Pull Requests.
## Using workflows from the catalog
To get started with a workflow from the catalog:
1. Clone the repository or download the specific workflow directory.
2. Review the documentation provided with the workflow to understand its requirements and usage.
3. Configure the workflow by editing the `config.yml` files as needed.
4. Execute the workflow using Snakemake.
For more detailed instructions, please refer to the documentation within each workflow directory.
## License
The Snakemake Workflow Catalog is open-source and available under the MIT License.
For more information and to explore the available workflows, visit https://snakemake.github.io/snakemake-workflow-catalog/.