The Agent Skills Directory

[COMMAND_EXECUTION]: The driver script scripts/run_gene_calling.py executes various bioinformatics CLI tools (e.g., pyrodigal, tRNAscan-SE, cmsearch) using the subprocess.run method. It correctly passes arguments as lists, which prevents shell injection risks that occur with string-based execution.
[EXTERNAL_DOWNLOADS]: The workflow integrates with BRAKER4 using Snakemake and Singularity, which may involve downloading containerized environments. The skill implements a security manifest (tool-manifest.json) to verify the integrity of the Snakemake configuration and container lock files using SHA256 checksums before any execution occurs.
[SAFE]: The skill demonstrates high-quality development practices, including robust validation of input manifests (checking file existence and integrity), safe handling of generated configuration files through idempotency checks, and clear documentation of tool versions and sources.

bio-gene-calling