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It performs multiple levels of analysis:\n\n1. **Basic Repository Checks**\n   - Repository cloning and validation\n   - README file verification\n   - Dependency file detection\n   - Test suite presence\n\n2. **Advanced Analysis**\n   - [Software Gardening Almanack](https://github.com/software-gardening/almanack) analysis\n   - JOSS (Journal of Open Source Software) criteria evaluation\n   - AI-powered repository analysis (optional, requires Synapse agent ID)\n   - Test execution and coverage\n\n3. **Optional Synapse Integration**\n   - Results upload to Synapse platform\n   - Metadata management\n\n## Requirements\n\n### Core Dependencies\n- **Nextflow** (version 24.04.3 or later): Install from [Nextflow's official website]. Install instructions below (https://www.nextflow.io/).\n- **Docker** (required for containerized execution): Install from [Docker's official website](https://www.docker.com/get-started).\n- **Python 3.8+**: Install from [Python's official website](https://www.python.org/downloads/).\n- **Git**\n\n\u003e [!IMPORTANT]\n\u003e Docker is required to run this workflow. The toolkit uses containerized processes to ensure consistent execution environments across different systems.\n\n### Optional Dependencies\nFor Synapse integration:\n- Synapse Python client\n- Synapse authentication token\n- Synapse configuration file\n\n## Installation\n\n1. **Install Nextflow**\n```bash\ncurl -s https://get.nextflow.io | bash\n```\n\n2. **Install Python Dependencies**\n```bash\npip install -r requirements.txt\n```\n\n3. **Configure Synapse** (Optional)\n```bash\n# Create Synapse config file\nmkdir -p ~/.synapse\ntouch ~/.synapseConfig\n```\n\n\u003e [!NOTE]\n\u003e To use Synapse features, you'll need to:\n\u003e 1. Create a personal access token from your [Synapse Account Settings](https://help.synapse.org/docs/Managing-Your-Account.2055405596.html#ManagingYourAccount-PersonalAccessTokens)\n\u003e 2. Add the token to your `~/.synapseConfig` file:\n\u003e    ```\n\u003e    [authentication]\n\u003e    username = your_username\n\u003e    apiKey = your_personal_access_token\n\u003e    ```\n\u003e 3. Set the token as a Nextflow secret:\n\u003e    ```bash\n\u003e    nextflow secrets set SYNAPSE_AUTH_TOKEN your_personal_access_token\n\u003e    ```\n\n## Usage\n\n### Input Format\n\nThe workflow accepts input in two formats:\n\n1. **Single Repository URL**\n```bash\nnextflow run main.nf --repo_url https://github.com/example/repo.git\n```\n\n2. **Sample Sheet (CSV)**\n\nExample `input.csv`:\n```csv\nrepo_url,description\nhttps://github.com/PythonOT/POT.git,Python Optimal Transport Library\nhttps://github.com/RabadanLab/TARGet.git,TARGet Analysis Tool\n```\n\n### Running the Workflow\n\n#### Basic Analysis\n```bash\nnextflow run main.nf --repo_url https://github.com/example/repo.git\n```\n\n#### With AI Analysis\n```bash\nnextflow run main.nf \\\n    --repo_url https://github.com/example/repo.git \\\n    --synapse_agent_id LOWYSX3QSQ\n```\n\n#### With Sample Sheet\n```bash\nnextflow run main.nf --sample_sheet input.csv\n```\n\n\u003e [!NOTE]\n\u003e When using AI Analysis or Synapse integration, ensure you have:\n\u003e - Valid Synapse authentication token\n\u003e - Proper Synapse configuration\n\u003e - Synapse agent ID for AI analysis (e.g., LOWYSX3QSQ)\n\u003e - Correct folder ID with write permissions (for upload)\n\n## Output\n\nThe workflow generates several output files in the `results` directory:\n\n- `\u003crepo_name\u003e_ai_analysis.json`: AI-powered qualitative summary and recommendations (final report)\n- `almanack_results.json`: Detailed metrics from Almanack analysis\n- `joss_report_\u003crepo_name\u003e.json`: JOSS criteria evaluation metrics\n- `test_results_\u003crepo_name\u003e.json`: Test execution results and coverage metrics\n\n\u003e [!NOTE]\n\u003e The AI analysis report provides a high-level qualitative summary and actionable recommendations. For detailed metrics and specific measurements, refer to the other output files.\n\n## Development Status\n\n\u003e [!WARNING]\n\u003e The AI Analysis component is currently in beta. Results may vary and the interface is subject to change.\n\n\u003e [!IMPORTANT]\n\u003e Synapse integration requires proper authentication and permissions setup.\n\n## Example Repositories\n\n| Repository | Description | Expected Status |\n|------------|-------------|----------------|\n| [PythonOT/POT](https://github.com/PythonOT/POT) | Python Optimal Transport Library | All checks pass |\n| [RabadanLab/TARGet](https://github.com/RabadanLab/TARGet) | TARGet Analysis Tool | Fails dependency and test checks |\n| [arjunrajlaboratory/memSeqASEanalysis](https://github.com/arjunrajlaboratory/memSeqASEanalysis) | memSeq ASE Analysis | Fails dependency and test checks |\n\n## Configuration\n\n### Synapse Configuration\n\n**Authentication Token**\n   - Set as Nextflow secret:\n   ```bash\n   nextflow secrets set SYNAPSE_AUTH_TOKEN your_personal_access_token\n   ```\n\n## Contributing\n\n\u003e [!NOTE]\n\u003e We welcome contributions! Please see our [Contributing Guidelines](CONTRIBUTING.md) for details.\n\n## License\n\nThis project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details. ","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmc2-center%2Fcckp-toolkit-workflow","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmc2-center%2Fcckp-toolkit-workflow","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmc2-center%2Fcckp-toolkit-workflow/lists"}