nf-bactopia

A Nextflow plugin for specifically for usage with Bactopia. It based of the modified nf-core libs and the nf-schema plugin.

This plugin will replicate the functionality of the previous libraries, while being compatible with future releases of Nextflow (>= 25).

Again, while you are free to do what you want, this plugin is specifically designed for Bactopia and will likely not work with other pipelines.

Setting up a Development Environment

Clone the repository

git clone [email protected]:bactopia/nf-bactopia.git

cd nf-bactopia

Create a new conda environment

conda create -y -n nf-bactopia \
    -c conda-forge \
    -c bioconda \
    make \
    'nextflow>=25'
conda activate nf-bactopia

Build the plugin and install

make assemble
make install

Use the plugin

The make install should put the plugin in your ~/.nextflow/plugins directory. So it should just work!

NXF_VER=25.06.0-edge nextflow run ...

Testing

This plugin has comprehensive test coverage with 230 unit tests covering 61.6% of the codebase.

Run tests

# Run all unit tests
./gradlew test

# Run tests with coverage report
./gradlew test jacocoTestReport

# View coverage report
open build/reports/jacoco/test/html/index.html

Coverage metrics

• Instruction Coverage: 61.6% (11,636 / 18,884 instructions)
• Method Coverage: 65.4%
• Class Coverage: 70.0%
• Total Tests: 230 (all passing ✓)

See docs/TESTING.md for detailed testing documentation.