dnanexus-integration

# DNAnexus Integration ## Overview DNAnexus is a cloud platform for biomedical data analysis and genomics. Build and deploy apps/applets, manage data objects, run workflows, and use the dxpy Python SDK for genomics pipeline development and execution. ## When to Use This Skill This skill should be used when: - Creating, building, or modifying DNAnexus apps/applets - Uploading, downloading, searching, or organizing files and records - Running analyses, monitoring jobs, creating workflows - Writing scripts using dxpy to interact with the platform - Setting up dxapp.json, managing dependencies, using Docker - Processing FASTQ, BAM, VCF, or other bioinformatics files - Managing projects, permissions, or platform resources ## Core Capabilities The skill is organized into five main areas, each with detailed reference documentation: ### 1. App Development **Purpose**: Create executable programs (apps/applets) that run on the DNAnexus platform. **Key Operations**: - Generate app skeleton with `dx-app-wizard` - Write Python or Bash apps with proper entry points - Handle input/output data objects - Deploy with `dx build` or `dx build --app` - Test apps on the platform **Common Use Cases**: - Bioinformatics pipelines (alignment, variant calling) - Data processing workflows - Quality control and filtering - Format conversion tools **Reference**: See `references/app-development.md` for: - Complete app structure and patterns - Python entry point decorators - Input/output handling...