The Agent Skills Directory

[COMMAND_EXECUTION]: The skill utilizes helper scripts like scripts/workflow_generator.py to create bash scripts which are then executed with chmod +x and direct invocation. This is a standard automation pattern for bioinformatics tools to manage multi-step analysis pipelines.
[DYNAMIC_EXECUTION]: The scripts/workflow_generator.py script dynamically assembles executable shell scripts from internal templates based on user parameters. This is used to facilitate the creation of complex deepTools commands for the user.
[INDIRECT_PROMPT_INJECTION]: The scripts/workflow_generator.py script takes parameters such as file paths and threads and interpolates them into bash script templates. While this represents a potential injection surface if malicious strings are provided as filenames, the risk is mitigated by the local nature of the execution and the specific use case for genomic data processing.
Ingestion points: Command-line arguments to scripts/workflow_generator.py.
Boundary markers: Absent in the generated shell script templates.
Capability inventory: Shell command execution and execution of generated scripts via SKILL.md instructions.
Sanitization: None detected in the template interpolation logic.

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