Nextflow Development

This is a workflow wrapper that lets you run nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) through Claude without writing pipeline code yourself. It handles the full stack: pulling datasets from GEO/SRA, environment checks, samplesheet generation, and pipeline execution with Docker. The checkpointed workflow is thoughtful, confirming genome selection and parameters before kicking off multi-hour jobs. It's aimed at bench scientists who need differential expression or variant calling but don't want to debug Nextflow configs. The implementation is explicitly marked as a prototype showing how to wrap one category of nf-core tools, not a production system, which is the right framing for something that automates compute-heavy analyses.