nextflow-development

MEDIUM W011: Third-party content exposure detected (indirect prompt injection risk).

• Third-party content exposure detected (high risk: 0.75). The required runtime workflow includes Step 0 “Acquire Data (GEO/SRA Only)”, which fetches study metadata and sample/run information from public NCBI GEO/SRA/ENA via python scripts/sra_geo_fetch.py info/download/samplesheet, and that fetched free-text metadata can be ingested into the agent’s context (e.g., displayed summaries and prompts for sample selection).

MEDIUM W012: Unverifiable external dependency detected (runtime URL that controls agent).

• Potentially malicious external URL detected (high risk: 1.00). The skill includes an installation step that runs a remote script via "curl -s https://get.nextflow.io | bash" (and similar curl -> bash instructions), which fetches and executes remote code at setup/runtime and is a required dependency for running the pipelines.