The Agent Skills Directory

[COMMAND_EXECUTION]: The script examples/sc_splicing_brie2.py uses subprocess.run to execute external bioinformatics CLI tools such as briekit-event, brie-count, and brie-quant.
Evidence: The skill defines Python functions that pass file paths directly to subprocess.run to invoke command-line utilities.
[EXTERNAL_DOWNLOADS]: The skill instructs the user to install several specialized packages directly from GitHub repositories rather than standard package registries.
Evidence: usage-guide.md includes commands for pip install git+https://github.com/songlab-cal/scquint, SpliZ, and psix, as well as R-based GitHub installations for MARVEL and Sierra.
[INDIRECT_PROMPT_INJECTION]: The skill is designed to ingest and process external data files (BAM, GTF, TSV) which could potentially contain malformed data or embedded instructions designed to influence agent behavior.
Ingestion points: examples/sc_splicing_brie2.py reads genomic BAM, GTF, and barcode files.
Boundary markers: None identified in the provided code to separate untrusted data from processing logic.
Capability inventory: The skill has the ability to execute shell commands and perform file system operations.
Sanitization: No explicit validation or sanitization of the contents of external genomic files is performed before they are passed to analytical tools.

bio-single-cell-splicing