Contributing¶

Contributions are welcome. This document describes how to set up a development environment and the conventions the project follows.

Development setup¶

git clone https://github.com/exterex/advena.git
cd advena

# Install Node.js dependencies (Prettier)
npm install

# Install and activate the pre-commit hooks
pip install pre-commit
pre-commit install

Code style¶

Nextflow (`.nf`, `.config`)¶

Nextflow files are formatted with Prettier via prettier-plugin-groovy.

Pre-commit hooks¶

The following hooks run automatically on git commit:

Hook	Purpose
`prettier`	Formatting for Nextflow, JSON, YAML, Markdown
`trailing-whitespace`	Strip trailing whitespace
`end-of-file-fixer`	Ensure files end with a newline
`check-yaml`	Validate YAML syntax
`check-json`	Validate JSON syntax
`mixed-line-ending`	Enforce LF line endings

Run all hooks manually:

pre-commit run --all-files

Testing¶

Stub run (fast, no software required)¶

nextflow run . -profile conda,test -stub-run

All 34 processes should complete successfully. This validates the channel topology without executing any real tools.

Full pipeline test¶

nextflow run . \
    --input assets/samplesheet.csv \
    --outdir results \
    -profile test,docker

Requires Docker and an accessible ICEscreen installation (ICESCREEN_ROOT).

nf-test¶

# requires Nextflow and Docker
nf-test test --profile docker --verbose

Tests live in tests/.

Branching and pull requests¶

main is the stable release branch.
Feature branches: feature/<description>
Bug/hot fixes: fix/<description>
Non-code tasks: chore/<description>
Preparing a release: release/<description>
Open a pull request against main; CI must pass before merge.

Releases¶

Releases follow Semantic Versioning. To cut a release:

Update the version in nextflow.config (manifest.version).
Commit with message release: bump version to X.Y.Z.
Push a X.Y.Z tag — the release.yml workflow creates the GitHub Release automatically.

git tag 1.1.0
git push origin 1.1.0