Spatial & Single-Cell Hackathon — CLI Scripts

This repo collects small CLI tools produced during the hackathon. The core expectation is simple:

• Put your CLI script in bin/.
• Add a matching atomic Dockerfile in docker/ that installs only what’s needed to run the CLI.
• If you need extra tooling, create a separate extended Dockerfile that builds on top of the atomic image.

Atomic image rule (practical)

• Atomic images should contain only runtime dependencies for the CLI.
• It’s OK to use pip in atomic images — just install the minimal packages needed to run the tool.
• Don’t add large, unrelated stacks (e.g., Java, ImageJ, Nextflow) to atomic images.
• If you need extras, make an extended multistage Dockerfile that FROM the atomic image and layers additional tools.

Optional extras

• Nextflow / nf-core modules are optional. If you build them, put them under optional/nextflow/ with a short README.
• Extended images (e.g., with OME-Zarr, Java, Nextflow) should live alongside atomic ones as separate *.extend.Dockerfile files.

Repository layout

├── bin/ # CLI entrypoints (bash/python), executable
│ ├── curate-spatial
│ ├── submit-bia
│ └── integrate-files
├── docker/ # One Dockerfile per CLI (atomic)
│ ├── curate-spatial.Dockerfile
│ ├── submit-bia.Dockerfile
│ ├── integrate-files.Dockerfile
│ └── <name>.extend.Dockerfile # optional: heavier variants built FROM the atomic image
├── templates/ # Schemas/examples for curation work
│ ├── bia-metadata.schema.json
│ └── sample-metadata.yaml
├── optional/
│ └── nextflow/ # optional modules/pipelines (not required)
└── README.md

Contribution checklist

1. Add your CLI to bin/NAME and make it executable.
2. Create docker/NAME.Dockerfile:
   • Install only the minimal runtime deps (OK to pip install the needed libs).
   • No unrelated heavyweight tools.
3. If you need extras, create docker/NAME.extend.Dockerfile that FROM ghcr.io/<org>/NAME:<tag> (or your local atomic tag) and adds those tools.
4. Update this README (or your tool’s mini-README) with a one-paragraph description and CLI --help.

Licensing

MIT by default (teams may adjust if required).