| name | nanocortex |
| description | Execute Oxford Nanopore and RNA workflows through OpenAI Codex 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, HPC workflow execution, validation, or biological summaries in Codex CLI. |
NanoCortex for OpenAI Codex
Install this directory at $CODEX_HOME/skills/nanocortex. Run tasks from the NanoCortex repository root with shell and filesystem access enabled (Auto-approve).
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.
Codex execution model
- Use the Codex shell tool for every command. Prefer one complete command per step.
- Record command, exit code, stderr, and output paths in the final response.
- Use absolute paths for inputs, outputs,
SKILL_DIR, and BOT_SIF.
- On non-zero exit, inspect stderr once, apply one targeted fix, and retry. Do not explore unrelated files.
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.
Singularity pattern
singularity exec <BOT_SIF> <TOOL> <ARGS>
For conda-backed tools:
singularity exec <BOT_SIF> bash -lc 'source /opt/conda/etc/profile.d/conda.sh && conda activate <ENV> && <TOOL> <ARGS>'
For Dorado, Modkit, or RNA-FM option lookup, use scripts/query_parameters.py with the bundled JSON specifications.
