Channel.fromBIDS Usage & Parameters

This page documents the Channel.fromBIDS factory call and runtime options.

Signature

Channel.fromBIDS(
	String bidsDir,
	String configPath = null,
	Map options = [:]
)

Required Parameters

Parameter Type Description

bidsDir

String

Path to the BIDS dataset root.

configPath

String

Path to the YAML configuration file.

Optional Runtime Options

Option Type Description

flatten_output

Boolean

Default true. Emits flat map items. Use false for legacy tuple format.

unpack_json_sidecar

Boolean

Default false. When true, JSON sidecars are emitted as parsed maps.

libbids_sh

String

Optional override path to libBIDS.sh.

use_bidsignore

Boolean

Whether to respect .bidsignore entries while parsing.

use_default_ignores

Boolean

Whether default ignore patterns are applied while parsing.

entity_aliases_json

String

Optional path to a JSON file used to enrich metadata aliases in emitted items.

bids_validation

Boolean

Validation toggle (reserved for validator integration flow).
Advanced validator-related options such as validator_version and ignore_codes are not part of the active user-facing runtime flow in the current release.

Basic Usage

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

workflow {
	Channel.fromBIDS(params.bids_dir, params.config)
		.view()
}

Usage with Runtime Options

Channel.fromBIDS(
	params.bids_dir,
	params.config,
	[
		flatten_output: true,
		unpack_json_sidecar: false,
		use_bidsignore: true,
		use_default_ignores: true,
		libbids_sh: null,
		entity_aliases_json: null
	]
)

Next Steps

  1. Configuration

  2. Output Shapes

  3. Examples