pacsomatic

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

• Third-party content exposure detected (low risk: 0.10). The runtime workflow in scripts/run_pacsomatic.py only ingests outsider-provided free text via explicit CLI arguments like --tumor-bam, --normal-bam, --patient-id, and --outdir to generate local artifacts, and it does not read from any external outsider-authored feed/queue/source without the user selecting/providing specific inputs.

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

• Potentially malicious external URL detected (high risk: 0.90). The skill can clone and/or run the nf-core/pacsomatic repository at runtime (git clone uses https://github.com/nf-core/pacsomatic.git and Nextflow may fetch/run that remote pipeline), which results in executing code fetched from that URL.