pacsomatic
Pass
Audited by Gen Agent Trust Hub on Oct 1, 2026
Risk Level: SAFECOMMAND_EXECUTIONEXTERNAL_DOWNLOADSDYNAMIC_EXECUTION
Full Analysis
- [COMMAND_EXECUTION]: The helper script
scripts/run_pacsomatic.pymanages the execution of external tools includingjava,git, and scheduler commands (sbatch,bsub,qsub). It handles the logic for submitting jobs to HPC environments. - [EXTERNAL_DOWNLOADS]: The skill clones the official nf-core/pacsomatic repository from GitHub to provide the pipeline source code. nf-core is a well-known community for bioinformatics workflows.
- [DYNAMIC_EXECUTION]: The skill dynamically generates a bash launch script tailored to the user's environment (local or HPC scheduler). This script encapsulates the Nextflow command and environment settings for reproducibility.
- [SAFE]: Robust security controls are implemented to prevent command injection. All user-supplied arguments are escaped using
shlex.quotebefore being written to the shell script. The--module-loadparameter is strictly validated against a blacklist of shell metacharacters and verified to start with a legitimate command.
Audit Metadata