pacsomatic
Operator toolkit for nf-core/pacsomatic matched tumor-normal workflows from BAM inputs. Use this skill when the user needs to validate run inputs, generate pacsomatic-compliant samplesheets, prepare reproducible Nextflow launch artifacts, run locally or submit to schedulers (LSF/Slurm/PBS/SGE), and triage execution failures. Triggers on requests to run pacsomatic, prepare launch commands/scripts, perform dry-run checks, or troubleshoot pipeline startup and scheduler submission errors.
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Low
Low-risk findings worth noting
Low
Low-risk findings.
1 low severity finding. Worth noting, but not necessarily harmful.
W012: Unverifiable external dependency detected (runtime URL that controls agent).
What this means
The skill fetches instructions or code from an external URL at runtime, and the fetched content directly controls the agent’s prompts or executes code. This dynamic dependency allows the external source to modify the agent’s behavior without any changes to the skill itself.
Why it was flagged
The script may perform a runtime git clone of https://github.com/nf-core/pacsomatic.git (scripts/run_pacsomatic.py constructs and runs `git clone args.repo_url`) and the fetched pipeline code can be executed later via Nextflow, so a remote repository URL is used at runtime to retrieve code that will be run.
- Repository
- K-Dense-AI/scientific-agent-skills
- Commit
36d8f13
- Audited
- Security analysis
Is this your skill?
If you maintain this skill, you can claim it as your own. Once claimed, you can manage eval scenarios, bundle related skills, attach documentation or rules, and ensure cross-agent compatibility.