The Agent Skills Directory

[COMMAND_EXECUTION]: The run_assembly_qc.py script executes external bioinformatics software such as SPAdes, Flye, metaMDBG, and QUAST using subprocess.run. The commands are constructed using a whitelist of tools and validated input paths from the assembly manifest.\n- [EXTERNAL_DOWNLOADS]: Documentation in the docs/ directory provides links to official GitHub repositories and websites for the assembly tools (e.g., SPAdes, Flye, Autocycler, QUAST). These references are for documentation and installation guidance and target well-known academic and open-source project locations.\n- [INDIRECT_PROMPT_INJECTION]: The skill processes external data which could influence its actions.\n
Ingestion points: run_assembly_qc.py reads data from the assemblies.tsv manifest file.\n
Boundary markers: Data is ingested via a structured TSV format; however, there are no explicit instructions to the agent to ignore embedded instructions within the fields.\n
Capability inventory: The skill can execute command-line tools via subprocess.run (in run_assembly_qc.py) and write files to the output directory.\n
Sanitization: The script performs validation on input paths (using resolve_file), checks modes against a defined set (MODES), and ensures unique sample_id values to prevent injection of malicious arguments.

bio-assembly-qc