nf-bactopia

Summary

A Nextflow plugin providing utility functions for Bactopia pipelines. It handles input collection, parameter validation, channel manipulation, and sample data transformation. Based on the modified nf-core libs and the nf-schema plugin, this plugin replicates the functionality of the previous Bactopia libraries while being compatible with Nextflow >= 25.

This plugin is specifically designed for Bactopia and will likely not work with other pipelines.

Get Started

Add the plugin to your nextflow.config:

plugins {
    id 'nf-bactopia'
}

Then import the functions you need in your Nextflow scripts:

include { bactopiaInputs     } from 'plugin/nf-bactopia'
include { bactopiaToolInputs } from 'plugin/nf-bactopia'
include { validateParameters } from 'plugin/nf-bactopia'
include { gather             } from 'plugin/nf-bactopia'
include { gatherCsvtk        } from 'plugin/nf-bactopia'
include { gatherFields       } from 'plugin/nf-bactopia'
include { formatSamples      } from 'plugin/nf-bactopia'
include { filterWithData     } from 'plugin/nf-bactopia'
include { collectNextflowLogs } from 'plugin/nf-bactopia'
include { combineWith        } from 'plugin/nf-bactopia'

Examples

Gathering outputs from a process

// Collect all TSV outputs from a process into a single record
gather(SCCMEC.out, 'tsv', [name: 'sccmec'])

// Gather and rename for CSVTK_CONCAT input
gatherCsvtk(ARIBA_RUN.out, 'report', [name: 'ariba-report', args: '-C "$" --lazy-quotes'])

// Gather multiple fields with explicit rename mapping
gatherFields(MODULE.out, [gff: 'gff', tsv: 'tsv'], [name: 'prokka'])

Filtering and combining channels

// Filter records where at least one field has data
filterWithData(MODULE.out, ['tsv', 'gff'])

// Cartesian product of gathered results with reference files
combineWith(gathered_ch, references_ch, 'reference')

Formatting samples for processes

// Adapt tuple sizes based on data availability
formatSamples(samples, 1)  // Returns [meta, inputs]
formatSamples(samples, 2)  // Returns [meta, inputs, extra]
formatSamples(samples, 3)  // Returns [meta, inputs, extra, extra2]

Development

Setting up a development environment

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

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

make assemble
make install

Testing

# 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

See docs/TESTING.md for detailed testing documentation.

License

MIT License. See LICENSE for details.