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nf-core/scge Pipeline
Cloud-native tumor-normal sequencing pipeline for the NIH Common Fund's Somatic Cell Genome Editing program. Built with Nextflow DSL2 and DRAGEN hardware acceleration on AWS.
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Nextflow AWS Batch DRAGEN nf-core Genomics
Co-developed a scalable Nextflow pipeline for the NIH Common Fund’s Somatic Cell Genome Editing (SCGE) program, adhering to strict nf-core reproducibility standards.
Architecture
- Nextflow DSL2 for modular, reusable workflow components
- Illumina DRAGEN hardware acceleration on AWS Batch for high-depth sequencing data processing
- nf-core conventions for reproducibility, testing, and CI/CD
- Docker/Singularity containerization for environment isolation
Key Achievements
- Minimized runtime for high-depth tumor-normal variant calling
- Full compliance with nf-core community standards
- Integrated with AWS Batch for elastic cloud compute scaling
- Handles petabyte-scale sequencing datasets with automated ingestion