Java Annotation Processing Task for Gradle forked from https://gist.github.com/nobuoka/7614981, fixed for Gradle 4.2 compatilbity, missing imports in JavaAptPlugin.groovy added, option to skip metadataGeneration for a subproject in a multi-project build added.

build.gradle

// java-apt プラグインを使うサンプル

apply plugin: 'java'
apply plugin: 'java-apt'

sourceCompatibility = '1.8'
targetCompatibility = '1.8'

tasks.withType(JavaCompile) {
    options.encoding = 'UTF-8'
}

repositories {
    mavenCentral()
}

buildscript {
    repositories {
        jcenter()
    }
    dependencies {
        classpath gradleApi()
    }
}

ext {
    generateMeta = true
}


dependencies {
    compile 'org.eclipse.persistence:org.eclipse.persistence.jpa:2.7.0'
    
    compile("org.eclipse.persistence:javax.persistence:2.1.1") {
      force = true
    }
    
    apt 'org.eclipse.persistence:org.eclipse.persistence.jpa.modelgen.processor:2.7.0'
}

procJava {
    def persistencexml = new File(project.projectDir, 'src/main/resources/META-INF/persistence.xml').absolutePath
    source    = project.compileJava.source
    processor = 'org.eclipse.persistence.internal.jpa.modelgen.CanonicalModelProcessor'
    apOptions = 'eclipselink.persistencexml=' + persistencexml
}

java-apt.properties

# buildSrc/src/main/resources/META-INF/gradle-plugins/java-apt.properties

implementation-class=JavaAptPlugin

JavaAptPlugin.groovy

// buildSrc/src/main/groovy/JavaAptPlugin.groovy

import org.gradle.api.DefaultTask
import org.gradle.api.Plugin
import org.gradle.api.Project
import org.gradle.api.internal.file.CompositeFileTree
import org.gradle.api.tasks.TaskAction
import org.gradle.api.tasks.compile.JavaCompile

class JavaAPT extends DefaultTask {
    private File _destinationDir

    def getDestinationDir(dir) { _destinationDir }

    void setDestinationDir(dir) {
        _destinationDir = dir
        outputs.dir _destinationDir
    }

    private CompositeFileTree _source

    def getSource() { _source }

    void setSource(CompositeFileTree src) {
        _source = src
        inputs.files src
    }

    String processor
    String apOptions

    @TaskAction
    void process() {
        if (project.properties.get('generateMeta') == true) {
            def javaCompile = project.task(name + "_", type: JavaCompile)
            javaCompile.source _source
            javaCompile.destinationDir = _destinationDir
            javaCompile.classpath = project.configurations.compile
            javaCompile.options.compilerArgs.addAll '-proc:only', '-implicit:none',
                    '-processorpath', project.configurations.apt.asPath,
                    '-processor', processor,
                    '-A' + apOptions

            javaCompile.execute()
            project.tasks.remove(javaCompile)
        }
    }
}

class JavaAptPlugin implements Plugin<Project> {
    void apply(Project project) {
        project.task('procJava', type: JavaAPT) {
            def defaultAptDestination = "build/generated-sources/metamodel"
            it.dependsOn project.configurations.compile
            project.tasks.compileJava.dependsOn it
            project.sourceSets.main.java.srcDirs << defaultAptDestination
            destinationDir = new File(project.projectDir, defaultAptDestination)
        }
        project.configurations {
            apt {
                description "for annotation processors"
            }
        }
    }
}