{"id":19227966,"url":"https://github.com/snakemake/snakemake-workflow-catalog","last_synced_at":"2026-06-26T15:30:19.417Z","repository":{"id":38363336,"uuid":"324645046","full_name":"snakemake/snakemake-workflow-catalog","owner":"snakemake","description":"A statically generated catalog of available Snakemake workflows","archived":false,"fork":false,"pushed_at":"2024-06-28T22:54:34.000Z","size":328237,"stargazers_count":28,"open_issues_count":5,"forks_count":10,"subscribers_count":6,"default_branch":"main","last_synced_at":"2024-06-29T00:15:36.672Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://snakemake.github.io/snakemake-workflow-catalog","language":"HTML","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/snakemake.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2020-12-26T22:25:08.000Z","updated_at":"2024-06-30T03:34:23.861Z","dependencies_parsed_at":"2023-10-03T17:04:41.398Z","dependency_job_id":"173f9c12-6b03-4c9e-b4bc-b60ca478bde8","html_url":"https://github.com/snakemake/snakemake-workflow-catalog","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/snakemake%2Fsnakemake-workflow-catalog","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/snakemake%2Fsnakemake-workflow-catalog/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/snakemake%2Fsnakemake-workflow-catalog/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/snakemake%2Fsnakemake-workflow-catalog/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/snakemake","download_url":"https://codeload.github.com/snakemake/snakemake-workflow-catalog/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":240302305,"owners_count":19779992,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-11-09T15:26:06.239Z","updated_at":"2026-06-26T15:30:19.351Z","avatar_url":"https://github.com/snakemake.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"# snakemake-workflow-catalog\n\n[![Generate catalog](https://github.com/snakemake/snakemake-workflow-catalog/actions/workflows/generate.yml/badge.svg)](https://github.com/snakemake/snakemake-workflow-catalog/actions/workflows/generate.yml)\n[![pages-build-deployment](https://github.com/snakemake/snakemake-workflow-catalog/actions/workflows/pages/pages-build-deployment/badge.svg)](https://github.com/snakemake/snakemake-workflow-catalog/actions/workflows/pages/pages-build-deployment)\n![GitHub last commit](https://img.shields.io/github/last-commit/snakemake/snakemake-workflow-catalog?label=latest%20update)\n![GitHub Issues or Pull Requests](https://img.shields.io/github/issues/snakemake/snakemake-workflow-catalog)\n\nA statically generated catalog of available Snakemake workflows\n\nThis 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.\n\n## Purpose\n\nThe 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:\n\n- Reproducibility: Snakemake workflows produce consistent results, making it easier to share and validate scientific findings.\n- Scalability: Snakemake workflows can be executed on various computing environments, from local machines to high-performance computing clusters and cloud services.\n- Modularity: Snakemake workflows are structured to allow easy customization and extension, enabling users to adapt them to their specific needs.\n\n## Workflows\n\nWorkflows 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.\n\n### All workflows\n\n- The workflow is contained in a public Github repository.\n- The repository has a `README.md` file, containing the words \"snakemake\" and \"workflow\" (case insensitive).\n- The repository contains a workflow definition named either `Snakefile` or `workflow/Snakefile`.\n- If the repository contains a folder `rules` or `workflow/rules`, that folder must at least contain one file ending on `.smk`.\n- 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).\n- The repository is not blacklisted here.\n\n### Standardized usage workflows\n\nIn order to additionally appear in the \"standardized usage\" area, repositories additionally have to:\n\n- 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),\n- provide configuration instructions under `config/README.md`\n- contain a `YAML` file `.snakemake-workflow-catalog.yml` in their root directory, which configures the usage instructions displayed by this workflow catalog.\n\nTypical content of the `.snakemake-workflow-catalog.yml` file:\n\n```bash\nusage:\n  mandatory-flags: # optional definition of additional flags\n    desc: # describe your flags here in a few sentences (they will be inserted below the example commands)\n    flags: # put your flags here\n  software-stack-deployment: # definition of software deployment method (at least one of conda, singularity, or singularity+conda)\n    conda: true # whether pipeline works with --use-conda\n    singularity: true # whether pipeline works with --use-singularity\n    singularity+conda: true # whether pipeline works with --use-singularity --use-conda\n    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\n```\n\nOnce 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=\u003cowner\u003e/\u003crepo\u003e`.\n\n### Release handling\n\nIf 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.\n\n## Contributing\n\nContributions to the Snakemake Workflow Catalog are welcome!\nIdeas 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.\n\n## Using workflows from the catalog\n\nTo get started with a workflow from the catalog:\n\n1. Clone the repository or download the specific workflow directory.\n2. Review the documentation provided with the workflow to understand its requirements and usage.\n3. Configure the workflow by editing the `config.yml` files as needed.\n4. Execute the workflow using Snakemake.\n\nFor more detailed instructions, please refer to the documentation within each workflow directory.\n\n## License\n\nThe Snakemake Workflow Catalog is open-source and available under the MIT License.\nFor more information and to explore the available workflows, visit https://snakemake.github.io/snakemake-workflow-catalog/.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsnakemake%2Fsnakemake-workflow-catalog","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsnakemake%2Fsnakemake-workflow-catalog","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsnakemake%2Fsnakemake-workflow-catalog/lists"}