pacsomatic

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

• Third-party content exposure detected (medium risk: 0.30). In scripts/run_pacsomatic.py, outsider-provided free text becomes LLM-readable when the user supplies fields like --extra-args, --module-load, --pipeline-version, and other CLI argument strings, which are then parsed/embedded into the generated Nextflow command/script via shlex.split() and string concatenation before execution.

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

• Potentially malicious external URL detected (high risk: 0.90). The helper can fetch and use the remote pipeline repository (default repo_url "https://github.com/nf-core/pacsomatic.git") at runtime—the script may git-clone that URL (ensure_pipeline_repo) or instruct Nextflow to fetch/run the remote pipeline—resulting in execution of externally fetched code.