The Agent Skills Directory

[INDIRECT_PROMPT_INJECTION]: The skill involves a data processing surface where it ingests outputs from various bioinformatic tools to generate summary tables.
Ingestion points: The scripts/build_bin_qc_tables.py script reads multiple TSV files (CheckM2, GUNC, EukCC, GTDB-Tk) provided as command-line arguments.
Boundary markers: None; data is processed as structured TSV/CSV format.
Capability inventory: The skill performs filesystem writes to a results/ directory via the Python script and tool executions.
Sanitization: The Python script uses the standard csv.DictReader for parsing and includes logic to validate domain routes and ensure identifiers are present, reducing the risk of processing malformed or malicious data structures.
[EXTERNAL_DOWNLOADS]: The skill provides instructions for fetching necessary scientific databases and software environments from reputable sources.
Downloads the CheckM2 database from Zenodo (DOI 10.5281/zenodo.14897628).
Fetches the EukCC2 database from the European Bioinformatics Institute (EBI) official FTP servers.
Pulls the BBTools container from the official repository maintained by Bryce Foster (bryce911/bbtools).
[COMMAND_EXECUTION]: The skill documentation includes examples of executing bioinformatic tools via Docker and local shell commands.
The recommended Docker command (docker run --rm -u "$(id -u):$(id -g)" -v "$PWD":/work ...) utilizes non-root user mapping and restricted volume mounting, which are standard security best practices for containerized workflows to prevent privilege escalation or unintended filesystem modifications.

bio-binning-qc