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, 'tsv', [name: 'sccmec'])

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

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

Filtering and combining channels

// Filter records where at least one field has data
filterWithData(MODULE, ['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]

License

MIT License. See LICENSE for details.