nf-bids Documentation

BIDS dataset integration and closure-based channel operators for Nextflow workflows.

nf-bids is a Nextflow plugin that parses BIDS (Brain Imaging Data Structure) datasets into typed Nextflow channels and provides closure-based operators for grouping and joining heterogeneous neuroimaging data.

Start Here

If you want to install and run the plugin in a workflow, start in:

User Guide

If you want plugin internals, architecture, testing, release, or API docs, use:

Development Overview

Quick Example

nextflow.config

plugins {
  id 'nf-bids@{plugin-version}'
}

main.nf

include { fromBIDS; groupTupleBy } from 'plugin/nf-bids'

workflow {
  Channel.fromBIDS(params.bids_dir, params.config)
    .groupTupleBy { it.meta.subject }
    .view()
}

The plugin targets Nextflow 24.10.0+, ships with libBIDS.sh v3.0 embedded, and is published on the Nextflow Plugin Registry.