Dependency Matrix

Nextflow

≥ 24.10.0

The workflow execution engine. Provides the nextflow.plugin.* SPI (pf4j), DataflowReadChannel / DataflowWriteChannel, Session, Channel.STOP, FileHelper.asPath(), and the @Factory / @Operator annotations that nf-bids uses to inject fromBIDS, groupTupleBy, joinBy, and combineBy into workflow scripts.

build.gradle: nextflowVersion = '24.10.0'

Groovy

4.0.23

The language in which all plugin classes are written. @CompileStatic is used throughout for compile-time type checking. Groovy 4 ships inside Nextflow’s classpath; the plugin does not bundle its own Groovy runtime.

README.md "Key Technologies" section

Java (JVM)

≥ 11 (Nextflow requirement)

Nextflow 24.10.x requires Java 11+. The plugin uses java.nio.file.Path, java.util.concurrent.CompletableFuture, and java.nio.file.Files. No Java source files exist; all production code is compiled Groovy.

Nextflow 24.10.0 release notes

GPars (groovyx.gpars)

Bundled with Nextflow

Provides DataflowQueue and DataflowWriteChannel. BidsHandler accumulates results in a DataflowQueue before binding them to the output channel; the *Op operator classes subscribe to DataflowReadChannel items.

Imported in BidsHandler.groovy, GroupTupleByOp.groovy, JoinByOp.groovy, CombineByOp.groovy

SnakeYAML

Bundled with Nextflow

Parses the bids2nf.yaml configuration file. BidsConfigLoader creates an org.yaml.snakeyaml.Yaml instance and calls yaml.load(FileReader).

BidsConfigLoader.groovy: import org.yaml.snakeyaml.Yaml

libBIDS.sh

v3.0

External bash library that walks the BIDS directory tree and emits a structured TSV. It is the only BIDS-file-inventory mechanism in the plugin; no Java-side directory scanning occurs. Bundled as a git submodule and included in the plugin ZIP via fileTree('libBIDS.sh') { include '*.sh' }.

.gitmodules (submodule URL), build.gradle (bundling), The libBIDS.sh Dependency

Bash

≥ 4.x (for set -euo pipefail and source)

Required at runtime on every machine where the plugin executes. LibBidsShWrapper invokes bash as ['bash', '-c', …​]; the libBIDSsh_parse_bids_to_table function requires bash 4 associative arrays.

LibBidsShWrapper.groovy: buildParseCommand()

Gradle Wrapper

8.14

The build system. Compiles Groovy sources, runs Spock/JUnit tests, assembles the plugin ZIP (via the io.nextflow.nextflow-plugin Gradle plugin), generates GroovyDoc, and orchestrates the Antora documentation build.

gradle/wrapper/gradle-wrapper.properties: distributionUrl=…​/gradle-8.14-bin.zip

Nextflow Plugin Gradle Plugin

1.0.0-beta.10

A custom Gradle plugin (io.nextflow.nextflow-plugin) that wires up plugin assembly, descriptor generation, and dependency bundling (including libBIDS.sh). Adds the nextflowPlugin {} DSL block used in build.gradle.

build.gradle: id 'io.nextflow.nextflow-plugin' version '1.0.0-beta.10'

PlantUML

Bundled as documentation/lib/plantuml.jar

Renders .puml diagram sources to SVG for inclusion in the Antora documentation site. Invoked by gradle/docs.gradle via the renderDiagrams task (bash bin/build-docs.sh --diagrams-only).

documentation/lib/plantuml.jar (file presence), gradle/docs.gradle

Antora

Installed via npm in documentation/

Renders the AsciiDoc documentation source tree into a static HTML site. Invoked by gradle/docs.gradle via the buildDocsSite task. documentation/node_modules/ confirms the npm install is present.

gradle/docs.gradle, documentation/node_modules/

Graphviz (dot)

System install

PlantUML delegates @startdot / @startuml diagram types to dot for graph layout. Required on the build machine when rendering package-dependency or sequence diagrams that use the dot engine. No version is pinned; PlantUML calls dot from PATH.

PlantUML documentation; used indirectly during renderDiagrams

Spock Framework

Bundled by Nextflow plugin Gradle plugin

The primary unit-test framework. Specification classes (*Spec.groovy) use Spock’s given/when/then notation. Examples: BidsConfigLoaderSpec, SuffixMapperSpec, BidsHandlerFlattenSpec.

src/test/groovy/nfneuro/**/*Spec.groovy

nf-test

Used for integration tests in validation/

Integration and validation tests that exercise Channel.fromBIDS() against real BIDS example datasets. Run separately with nf-test test validation/.

nf-test.config, README.md contributing section

BIDS Validator

Not implemented (v1.1)

BidsValidator.groovy exists as a stub. Its validate() method logs a warning and returns immediately. The validation call in BidsChannelFactory is commented out. When implemented, this will invoke bids-validator (likely via Docker) before parsing begins.

BidsValidator.groovy class-level javadoc, BidsChannelFactory.groovy commented block

Nextflow

24.10.0

Runtime

Groovy

4.0.23 (via Nextflow)

Runtime

Java JVM

11

Runtime

GPars

via Nextflow

Runtime

SnakeYAML

via Nextflow

Runtime

libBIDS.sh

v3.0

Runtime

Bash

4.x

Runtime

Gradle Wrapper

8.14

Build

Nextflow Plugin Gradle Plugin

1.0.0-beta.10

Build

PlantUML

(bundled jar)

Build (docs)

Antora

(npm)

Build (docs)

Graphviz

any

Build (docs)

Spock

via Gradle plugin

Test

nf-test

any recent

Test (integration)