{"id":28293408,"url":"https://github.com/getwilds/wilds-wdl-library","last_synced_at":"2026-02-01T11:33:14.606Z","repository":{"id":294762987,"uuid":"986639753","full_name":"getwilds/wilds-wdl-library","owner":"getwilds","description":"Collection of bioinformatics-related WDL workflow for use in WILDS","archived":false,"fork":false,"pushed_at":"2025-06-12T23:49:21.000Z","size":225,"stargazers_count":0,"open_issues_count":12,"forks_count":0,"subscribers_count":0,"default_branch":"main","last_synced_at":"2025-06-13T00:36:53.476Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"WDL","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/getwilds.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":".github/CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":".github/CODE_OF_CONDUCT.md","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,"zenodo":null}},"created_at":"2025-05-19T23:11:23.000Z","updated_at":"2025-06-10T05:16:39.000Z","dependencies_parsed_at":"2025-06-13T00:28:13.805Z","dependency_job_id":"68943432-9120-4dfa-a705-d4cf7aedefcb","html_url":"https://github.com/getwilds/wilds-wdl-library","commit_stats":null,"previous_names":["getwilds/wilds-wdl-library"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/getwilds/wilds-wdl-library","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/getwilds%2Fwilds-wdl-library","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/getwilds%2Fwilds-wdl-library/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/getwilds%2Fwilds-wdl-library/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/getwilds%2Fwilds-wdl-library/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/getwilds","download_url":"https://codeload.github.com/getwilds/wilds-wdl-library/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/getwilds%2Fwilds-wdl-library/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":259729337,"owners_count":22902577,"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":"2025-05-22T06:13:04.781Z","updated_at":"2026-02-01T11:33:14.599Z","avatar_url":"https://github.com/getwilds.png","language":"WDL","funding_links":[],"categories":[],"sub_categories":[],"readme":"\u003ctable\u003e\n\u003ctr\u003e\n  \u003ctd style=\"width: 400px; max-width: 400px;\"\u003e\u003cimg src=\"https://raw.githubusercontent.com/getwilds/wilds-wdl-library/main/WILDSWDLLogo.jpeg\" width=\"400\" alt=\"WILDS WDL logo\"\u003e\u003c/td\u003e\n  \u003ctd style=\"vertical-align: middle;\"\u003e\n    \u003ch1\u003eWILDS WDL Library\u003c/h1\u003e\n    \u003cp\u003eA centralized collection of bioinformatics WDL infrastructure providing reusable, well-tested components that can be combined to create powerful computational pipelines for genomics research.\u003c/p\u003e\n  \u003c/td\u003e\n\u003c/tr\u003e\n\u003c/table\u003e\n\n[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)\n[![Project Status: Prototype – Useable, some support, open to feedback, unstable API.](https://getwilds.org/badges/badges/prototype.svg)](https://getwilds.org/badges/#prototype)\n[![WDL Executors](https://img.shields.io/badge/WDL-Cromwell%20%7C%20miniWDL%20%7C%20Sprocket-blue.svg)](https://github.com/getwilds/wilds-wdl-library)\n[![WDL](https://img.shields.io/badge/WDL-1.0-orange.svg)](https://openwdl.org/)\u003cbr\u003e\n[![Module Tests](https://github.com/getwilds/wilds-wdl-library/actions/workflows/modules-testrun.yml/badge.svg)](https://github.com/getwilds/wilds-wdl-library/actions/workflows/modules-testrun.yml)\n[![Pipeline Tests](https://github.com/getwilds/wilds-wdl-library/actions/workflows/pipelines-testrun.yml/badge.svg)](https://github.com/getwilds/wilds-wdl-library/actions/workflows/pipelines-testrun.yml)\n[![Linting](https://github.com/getwilds/wilds-wdl-library/actions/workflows/linting.yml/badge.svg)](https://github.com/getwilds/wilds-wdl-library/actions/workflows/linting.yml)\n\n## Overview\n\nThe WILDS WDL Library consolidates bioinformatics workflows into a single, well-organized repository that serves as both a collection of production-ready tools and a demonstration of WDL best practices. Rather than maintaining separate repositories for each workflow, this library promotes modularity and reusability through a two-tier architecture.\n\n## Library Architecture\n\nThe library is organized into two complementary levels:\n\n### **Modules** (`modules/`)\nTool-specific collections of reusable WDL tasks with comprehensive testing.\n- **Purpose**: Foundational building blocks for larger workflows\n- **Content**: Individual bioinformatics tools (STAR, BWA, GATK, etc.)\n- **Testing**: Unit tests ensure each task functions correctly over time\n- **Usage**: Import tasks into custom workflows or run demonstration workflows\n\n### **Pipelines** (`pipelines/`)\nComplete analysis workflows combining multiple modules.\n- **Purpose**: Functional pipelines ranging from educational examples to production-ready analyses\n- **Content**: Multiple modules combined into analysis workflows of varying complexity\n- **Complexity Levels**: Basic (2-3 modules), Intermediate (4-6 modules), Advanced (10+ modules)\n- **Testing**: Integration tests verify modules work together seamlessly\n- **Usage**: Templates for common workflows, learning examples, or production analyses\n\n## Quick Start\n\n### Running Pipelines Directly (No Clone Required)\n\nThanks to GitHub URL imports, you can download and run any pipeline without cloning the entire repository:\n\n```bash\n# Download a pipeline and its example inputs\n# Option 1: Use curl from the command line\ncurl -O https://raw.githubusercontent.com/getwilds/wilds-wdl-library/main/pipelines/ww-sra-star/ww-sra-star.wdl\ncurl -O https://raw.githubusercontent.com/getwilds/wilds-wdl-library/main/pipelines/ww-sra-star/inputs.json\n# Option 2: Download directly from GitHub by navigating to the file and clicking the download button\n\n# Modify inputs.json as necessary for your data, then run via the command line or PROOF's point-and-click interface\nsprocket run ww-sra-star.wdl inputs.json\n```\n\n### Using the Full Repository\n\nIf you want to explore multiple components or contribute:\n\n```bash\n# Clone the repository\ngit clone https://github.com/getwilds/wilds-wdl-library.git\ncd wilds-wdl-library\n\n# Run a module test workflow (no inputs needed)\ncd modules/ww-star\nsprocket run testrun.wdl\n\n# Run a pipeline (modify inputs.json as necessary)\ncd ../../pipelines/ww-sra-star\nsprocket run ww-sra-star.wdl inputs.json\n```\n\n### Importing into Your Workflows\n\n```wdl\nimport \"https://raw.githubusercontent.com/getwilds/wilds-wdl-library/refs/heads/main/modules/ww-sra/ww-sra.wdl\" as sra_tasks\nimport \"https://raw.githubusercontent.com/getwilds/wilds-wdl-library/refs/heads/main/modules/ww-star/ww-star.wdl\" as star_tasks\n\nworkflow my_analysis {\n  call sra_tasks.fastqdump { input: sra_id = \"SRR12345678\" }\n  call star_tasks.star_align_two_pass {\n    input: sample_data = { \"name\": \"sample1\", \"r1\": fastqdump.r1_end, \"r2\": fastqdump.r2_end }\n  }\n}\n```\n\nWILDS pipelines use GitHub URLs for imports, providing several advantages:\n\n- **No local cloning required**: Use modules directly without downloading the repository\n- **Version control**: Pin to specific commits or tags for reproducibility\n- **Easy updates**: Switch between versions by changing the URL\n- **Modular usage**: Import only the modules you need\n\n## Supported Executors\n\nAll components are tested with multiple WDL executors:\n- **[Sprocket](https://sprocket.bio/)**: Modern WDL executor with enhanced features\n- **[Cromwell](https://cromwell.readthedocs.io/)**: Production-grade workflow engine\n- **[miniWDL](https://github.com/chanzuckerberg/miniwdl)**: Lightweight local execution\n\n## For Fred Hutch Users\n\nFred Hutch researchers can use [PROOF](https://sciwiki.fredhutch.org/dasldemos/proof-how-to/) to submit workflows directly to the on-premise HPC cluster. This provides a user-friendly interface for researchers unfamiliar with command-line tools while leveraging the power of the institutional computing resources.\n\n**Cromwell Configuration**: PROOF users can customize workflow execution using Cromwell options. See [cromwell-options.json](cromwell-options.json) for example configurations including call caching, output directories, and more. For detailed information, refer to the [Cromwell workflow options documentation](https://cromwell.readthedocs.io/en/stable/wf_options/Overview/).\n\n**Platform-Specific Configurations**: Some pipelines include optional platform-specific configurations (e.g., `.cirro/` directories) for execution on cloud platforms like [Cirro](https://cirro.bio/). These configurations are self-contained within each pipeline directory.\n\n## Quality Assurance\n\n### Automated Testing\n- **Continuous Integration**: All components tested on every pull request\n- **Multi-Executor Validation**: Ensures compatibility across different WDL engines\n- **Real Data Testing**: Uses authentic bioinformatics datasets for validation\n- **Scheduled Monitoring**: Weekly checks detect infrastructure changes\n\n### Standards and Best Practices\n- **Standardized Structure**: Consistent organization across all components\n- **Container Management**: Versioned, tested Docker images from the [WILDS Docker Library](https://github.com/getwilds/wilds-docker-library)\n- **Documentation Standards**: Comprehensive README files and inline documentation\n- **Version Control**: Semantic versioning and careful dependency management\n\n## Contributing\n\nWe welcome contributions at all levels:\n\n### Adding New Modules\n1. Focus on high-utility bioinformatics tools\n2. Follow the standard module structure\n3. Include comprehensive tests and validation\n4. Provide detailed documentation\n\n### Creating Pipelines\n1. Combine existing modules (prefer existing modules over new tasks)\n2. Demonstrate common analysis patterns\n3. Include realistic test datasets\n4. Document complexity level and integration approaches\n\n### Improving Documentation\n- Enhance existing README files\n- Add usage examples and tutorials\n- Improve inline code documentation\n- Contribute to the [WILDS documentation site](https://getwilds.org/)\n\nSee our [Contributing Guidelines](.github/CONTRIBUTING.md) and the [WILDS Contributor Guide](https://getwilds.org/guide/) for detailed information.\n\n## Development Roadmap\n\n### Current Focus\n- Expanding the module collection with high-priority tools (GATK variant calling, additional alignment tools)\n- Adding new pipelines across all complexity levels\n- Enhancing testing infrastructure and validation\n\n### Future Plans\n- Additional advanced pipelines for publication-ready analyses\n- Enhanced integration with Fred Hutch computing infrastructure\n- Community-contributed modules and pipelines\n- Advanced documentation and tutorial content\n\n## Support\n\n- **Issues and Bug Reports**: [GitHub Issues](https://github.com/getwilds/wilds-wdl-library/issues)\n- **General Questions**: Contact the Fred Hutch Data Science Lab at wilds@fredhutch.org\n- **Documentation**: [WILDS Guide](https://getwilds.org/guide/)\n- **Fred Hutch Users**: [Scientific Computing Wiki](https://sciwiki.fredhutch.org/)\n\n## Related Resources\n\n- **[WILDS Docker Library](https://github.com/getwilds/wilds-docker-library)**: Container images used by WDL workflows\n- **[WILDS Documentation](https://getwilds.org/)**: Comprehensive guides and best practices\n- **[Fred Hutch SciWiki](https://sciwiki.fredhutch.org/)**: Institutional computing resources and tutorials\n\n## License\n\nDistributed under the MIT License. See `LICENSE` for details.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgetwilds%2Fwilds-wdl-library","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgetwilds%2Fwilds-wdl-library","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgetwilds%2Fwilds-wdl-library/lists"}