What the reviewer found
NGS bioinformatics pipeline guide. `curl -s https://get.nextflow.io | bash` is Nextflow's own official installer from get.nextflow.io, `rm -rf /var/lib/apt/lists/*` is the standard Dockerfile apt-cache cleanup idiom, and the wget/curl/samtools line is just an `apt-get install` package list. All are ordinary build/setup steps, nothing destructive or external beyond installing named tools.
installs-software— installs software
What was read
The file as it ships in Lord1Egypt/scientific-agent-toolkit:
scientific-skills/ngs-pipeline-management/SKILL.md
What the static scan said
The scan flagged 3things. The reviewer kept 0 and dismissed 3 as false.
SC2Downloads and executes remote code — false positiveRMRecursive force delete — false positiveNETMakes network calls — false positive
How this review was made
Sonnet 5 read the files above on 7 September 2026 and answered three questions: is it dangerous to whoever installs it, is each scanner finding real, and what should the installer know. The verdict is bound to the file's hash; when the file changes, it is scanned afresh and reviewed again. A script that changes while the definition does not is not re-reviewed — that is a known gap. How the scan and the review work.