| name | nanocortex |
| description | Execute Oxford Nanopore and RNA workflows in Gemini ADK with NanoCortex's Singularity image, including Dorado, Modkit, transcript/splicing analysis, RNA-FM structure prediction, and Remora signal plotting. Use for nanopore BAM/BED, GTF isoforms, RNA FASTA, POD5 signal plots, ADK agent workflows, validation, or biological summaries in Gemini. |
NanoCortex for Gemini ADK
Load this directory as the instruction context for a Gemini ADK agent deployed on Linux with filesystem and shell access (Always Allow). Run tasks from the NanoCortex repository root.
Default container: singularity/bot.sif relative to the NanoCortex repository. Do not install alternative software when the container is available.
Read references/environment.md only when the direct Singularity command is unavailable.
Gemini ADK execution model
- Route signal-plotting requests to
agents/signal_agent.py when using the native ADK agent graph.
- For all other workflows, follow the reference files and execute commands through the ADK code-execution tool.
- Use absolute paths for inputs, outputs,
SKILL_DIR, and BOT_SIF.
- Preserve command records, exit codes, stderr excerpts, and validation results in the agent response.
- On failure, apply one targeted correction from stderr, then retry.
Fast path
- Identify the task from the request and input suffix.
- Read exactly one reference:
- Prefer bundled scripts. Run
python3 <SKILL_DIR>/scripts/<script>.py --help before use.
- Verify the selected container tool once with
--help or --version, then execute.
- Validate outputs with the bundled validator or the checks in the selected reference.
- Return method, parameters, main results, output paths, and limitations.
For Dorado, Modkit, or RNA-FM option lookup, use scripts/query_parameters.py with the bundled JSON specifications.
