| name | nanocortex |
| description | Execute Oxford Nanopore and RNA workflows in Claude Code 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, Singularity execution, validation, or biological summaries in Claude Code. |
NanoCortex for Claude Code
Install this directory at ~/.claude/skills/nanocortex (personal) or .claude/skills/nanocortex (project). Run tasks from the NanoCortex repository root with Bash and file-access permissions approved.
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.
Claude Code execution model
- Use the Bash tool for all shell and Singularity commands.
- Request only the permissions needed for the current step. Do not batch unrelated filesystem access.
- Use absolute paths for inputs, outputs,
SKILL_DIR, and BOT_SIF.
- Keep a concise execution log: command, exit code, stderr summary, and output paths.
- On failure, inspect stderr once, apply one targeted fix, and 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.
