dnanexus-integration
Integrate DNAnexus genomics platform workflows
Also available from: davila7
DNAnexus provides cloud-based genomics analysis but requires platform-specific knowledge. This skill offers complete documentation for building apps, managing data, and running bioinformatics workflows.
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Using "dnanexus-integration". How do I upload a FASTQ file and run quality control?
Expected outcome:
- 1. First authenticate: dx login
- 2. Upload your file: dx upload sample.fastq --project project-xxxx
- 3. Find a QC applet: dx find_applets --name '*qc*'
- 4. Run analysis: dx run applet-xxxx -i reads=file-yyyy
- 5. Monitor progress: dx watch job-zzzz
- 6. Download results when complete
Using "dnanexus-integration". Create a simple app that filters reads by quality
Expected outcome:
- Define dxapp.json with inputSpec for reads file and outputSpec for filtered reads
- Use @dxpy.entry_point('main') decorator for the main function
- Download input with dxpy.download_dxfile()
- Process with subprocess.call() to external tool
- Upload output with dxpy.upload_local_file()
- Return result using dxpy.dxlink()
Security Audit
SafeAll 455 static findings are false positives. The skill is documentation for DNAnexus cloud genomics platform. The flagged 'external_commands' are legitimate DNAnexus CLI commands (dx, dxpy) in documentation code blocks. The 'weak cryptographic algorithm' findings incorrectly identified API version fields like 'dxapi: 1.0.0' as cryptographic code. The 'Windows SAM database' alert misidentified authentication documentation (DX_SECURITY_CONTEXT) as Windows system files. No malicious patterns exist.
Risk Factors
⚙️ External commands (5)
🌐 Network access (1)
Quality Score
What You Can Build
Process sequencing data pipeline
Upload FASTQ files, run alignment and variant calling workflows, download results for research analysis
Build custom analysis apps
Create DNAnexus apps for specialized genomics analyses with proper input and output handling
Organize genomic datasets
Search, categorize, and manage large genomic datasets across multiple DNAnexus projects
Try These Prompts
Help me upload a FASTQ file to DNAnexus and run a basic quality control analysis using an existing applet
I need to create a DNAnexus app that takes FASTQ input and outputs BAM alignment using BWA-MEM
Show me how to find all FASTQ files in a project and run the same analysis on each in parallel
Help me configure dxapp.json for an app that needs samtools, bcftools, and a custom Docker image with reference genomes
Best Practices
- Always validate input files before processing in DNAnexus apps
- Use appropriate DNAnexus instance types for compute-intensive analyses
- Include comprehensive error handling and logging in custom apps
Avoid
- Hardcoding project IDs or file paths in production apps
- Processing large files without checking available disk space
- Ignoring DNAnexus job states and error conditions