The Agent Skills Directory

[COMMAND_EXECUTION]: The helper script scripts/run_pacsomatic.py invokes system utilities such as git, java, and cluster schedulers (Slurm, LSF, etc.) using subprocess.run. These operations are required for pipeline setup and submission and are performed using secure argument-passing methods to prevent shell injection.\n- [EXTERNAL_DOWNLOADS]: The skill is configured to clone the nf-core/pacsomatic pipeline repository from its official GitHub source. This is a common and necessary step for deploying bioinformatics workflows and involves a well-known community repository.\n- [INDIRECT_PROMPT_INJECTION]: The skill handles user-provided data such as file paths and sample identifiers. Potential injection vectors are mitigated through comprehensive sanitization routines, including the use of shlex.quote for shell script assembly and a restrictive character skip-list for the --module-load parameter to ensure only valid module commands are processed.

pacsomatic