The Agent Skills Directory

[SAFE]: The skill's primary purpose is the management and execution of bioinformatics workflows using the established deeptools Python package. All included scripts and documentation align with this legitimate purpose.
[COMMAND_EXECUTION]: The skill frequently uses shell commands to interact with bioinformatics tools (e.g., bamCoverage, plotHeatmap). These are standard operations for the intended use case. The scripts/workflow_generator.py script automates the creation of these command sequences based on user-provided parameters.
[EXTERNAL_DOWNLOADS]: The skill instructions include uv pip install deeptools to install the necessary library from a standard package registry. It also references official documentation at deeptools.readthedocs.io and ENCODE guidelines, which are trusted sources in the genomics community.
[INDIRECT_PROMPT_INJECTION]: The scripts/validate_files.py script reads the first 10 lines of user-provided BED files to verify formatting. While this constitutes processing of untrusted external data, the scope is limited and intended for structural validation rather than content interpretation, presenting a negligible risk of prompt injection.

deeptools