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 the Nextflow strict syntax (Nextflow version >= 24).

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 git@github.com:bactopia/nf-bactopia.git

cd nf-bactopia

Create a new conda environment

conda create -n nf-bactopia \
    -c conda-forge \
    -c bioconda \
    gradle \
    make \
    'nextflow>=24'