The Agent Skills Directory

[COMMAND_EXECUTION]: The scripts/run_pacsomatic.py script executes various system utilities including java, git, nextflow, and HPC scheduler commands (sbatch, bsub, qsub) using the subprocess module. The implementation uses list-based arguments to prevent shell injection vulnerabilities.
[EXTERNAL_DOWNLOADS]: The script is designed to clone the nf-core/pacsomatic pipeline repository from GitHub. This targets a well-known bioinformatics organization and the operation is triggered by explicit user configuration flags.
[DYNAMIC_EXECUTION]: The helper generates a bash launch script at runtime based on user-provided parameters and subsequently executes it. The script utilizes shlex.quote and a custom metacharacter filter (_SHELL_METACHARACTERS) to sanitize inputs before they are written into the executable shell script.
[INDIRECT_PROMPT_INJECTION]: The skill ingests external data, such as sample identifiers and file paths, which are incorporated into command-line arguments and generated scripts.
Ingestion points: Command-line arguments processed in scripts/run_pacsomatic.py (e.g., --tumor-bam, --patient-id).
Boundary markers: The script enforces strict validation rules, ensuring identifiers contain no whitespace or control characters.
Capability inventory: The script possesses capabilities to write files to the local filesystem and execute subprocesses (git, nextflow, scheduler binaries).
Sanitization: Inputs are sanitized using shlex.quote during script generation and list-based subprocess.run calls for direct execution.

pacsomatic