nanorunner is a Python tool that delivers FASTQ files into a target directory with controlled timing, so that watch-directory analysis pipelines can be exercised without an active sequencer.
- Getting started -- install, the two run modes, and a first end-to-end run.
- Replay guide -- transferring existing FASTQ files, rechunking, and the 3x3 input/output reshape matrix.
- Generate guide -- simulating reads from genomes, species names, and mock communities.
- Timing models -- the four timing models and the available profiles.
- Pipeline integration -- driving Nanometa Live, nanometanf, and Kraken from nanorunner.
- CLI reference -- every option grouped by purpose.
- Configuration reference -- field
tables for
ReplayConfigandGenerateConfig. - Troubleshooting -- installation, runtime, and dependency issues.
- Testing notes -- test categories and conventions.
- CLAUDE.md -- developer guide (architecture, extension points).
- Examples -- runnable scripts.
- Archive -- historical audits and design plans.
- Nanometa Live walkthrough -- end-to-end demo driving Nanometa Live with simulated reads.
- Current version: 3.1.0
- Python requirement: 3.9 or later
- Test coverage: 91%