pacsomatic
No security findings. Scanned 1 time, most recently 2026-10-21.
Second scanner: NVIDIA SkillSpector
Independent static run, no language model, over the same files as the Cisco scan above. How the two scanners compare across the whole corpus: Two scanners, one corpus.
What this skill does
Prepares and launches nf-core/pacsomatic matched tumor-normal PacBio HiFi genomics workflows from unaligned BAM inputs. Supports samplesheet generation, pinned Nextflow launch artifacts, local checks, LSF/Slurm/PBS Pro/SGE launcher submission, and startup troubleshooting. Use for pacsomatic run preparation and execution, not general short-read somatic analysis or medical imaging PACS.
- Package
- 7 files, 57 KB
- SKILL.md
- 669 words, 5 sections
- Code
- Python (1)
- License
- MIT
- Compatibility
- Requires Python 3.10+ for the standard-library helper. Execution requires Bash, Nextflow >=24.04.2, a compatible Java runtime (current Nextflow supports Java 17-26), the selected container runtime and optionally a scheduler. Network access is needed for uncached pipeline code, plugins, references and containers.
SKILL.md covers: pacsomatic · When to use · Workflow · Examples · Verification and references
Findings
No findings. SAFE
What is in the package
| File | Kind | Size |
|---|---|---|
LICENSE | other | 1.0 KB |
SKILL.md | doc | 6.3 KB |
config.yaml | config | 1.0 KB |
references/agent-playbook.md | doc | 2.0 KB |
references/config-and-output.md | doc | 5.8 KB |
references/pacsomatic_guide.md | doc | 5.2 KB |
scripts/run_pacsomatic.py | script | 36 KB |
External hosts referenced
github.com docs.seqera.io nf-co.re pacbiofileformats.readthedocs.io www.ibm.com slurm.schedmd.com
Hostnames that appear in the skill's files. Referencing a host is not a finding; compare against the findings above and the skill's stated purpose.
Environment variables referenced
JAVA_HOME
Package contents recorded 2026-10-22 at commit 593377bb0487. The scan above ran against the version current at scan time; the two can differ if the skill has since been updated.
What we checked
- Static analyzer. Pattern rules over SKILL.md and bundled files: known-bad commands, exfiltration URLs, secrets, obfuscation.
- Bytecode analyzer.
- Pipeline analyzer.
- Correlation analyzer.
- Behavioral analyzer. Checks what the skill asks the agent to do against what its description claims it does.
- Trigger analyzer. Looks for instructions that fire on conditions the user did not ask for.
What we did not check
- Runtime behaviour. The skill was not executed; findings come from reading its files.
- Anything fetched at install or run time, including remote scripts, package dependencies, and URLs the skill tells the agent to open.
- Content the analyzers cannot read: images, binaries, and some non-English text.
- Known scanner bypass classes. See the methodology and limitations page.
Sources
- Repository: https://github.com/K-Dense-AI/scientific-agent-skills
- Raw scan result: skills-pacsomatic-scan.json
- Badge for your README:
- Request a re-scan