name: bio-gene-calling description: Call genes and annotate basic features for prokaryotes, viruses, and eukaryotes.

Bio Gene Calling

Call genes and annotate basic features for prokaryotes, viruses, and eukaryotes.

Task	Action
Run workflow	Follow the steps in this skill and capture outputs.
Validate inputs	Confirm required inputs and reference data exist.
Review outputs	Inspect reports and QC gates before proceeding.
Tool docs	See `docs/README.md`.
References	- See ../bio-skills-references.md

Prerequisites:

Tools available in the active environment (Pixi/conda/system). See docs/README.md for expected tools.
Input contigs or bins are available. Inputs:
contigs.fasta or bins/*.fasta

Gene count sanity checks pass.
Start/stop codon checks pass.
On failure: retry with alternative parameters; if still failing, record in report and exit non-zero.
Verify contigs are non-empty and DNA alphabet.
Verify outputs contain expected feature types.

contigs.fasta or bins/*.fasta

Issue: Missing inputs or reference databases Solution: Verify paths and permissions before running the workflow.

Issue: Low-quality results or failed QC gates Solution: Review reports, adjust parameters, and re-run the affected step.

Name	bio-gene-calling
Description	Call genes and annotate basic features for prokaryotes, viruses, and eukaryotes.