bio-gene-callinglisted

# Bio Gene Calling Call genes and annotate basic features for prokaryotes, viruses, and eukaryotes. ## Instructions 1. Validate the assembly and tool manifests, then generate a per-assembly execution plan: ```bash uv run --no-project python skills/bio-gene-calling/scripts/run_gene_calling.py \ assemblies.tsv --tool-manifest tool-manifest.json \ --out results/bio-gene-calling # Inspect run_manifest.json, then execute or resume the same plan: uv run --no-project python skills/bio-gene-calling/scripts/run_gene_calling.py \ assemblies.tsv --tool-manifest tool-manifest.json \ --out results/bio-gene-calling --execute ``` The tool manifest must pin the BRAKER4 repository commit, Snakefile checksum, container-lock checksum, and every Rfam model checksum. The driver records input FASTA checksums, routes each assembly by domain, writes idempotent BRAKER4 `samples.csv` and `config.ini` files, uses absolute covariance-model paths, and materializes the required default/relaxed ncRNA census rows. Execution reuses only non-empty declared outputs and replaces pending ncRNA counts with parsed tRNAscan-SE and Infernal counts. 2. Select gene caller by organism class: - Bacteria and Archaea: **Pyrodigal** v3.7+ with single-genome or metagenomic mode chosen from the input. - Viruses, including giant and alternative-code viruses: **pyrodigal-gv** v0.3+ with the appropriate viral model. - Eukaryotes: **BRAKER4** as the current upstream workflow. P