Java Annotation Processing Task for Gradle

build.gradle

// java-apt プラグインを使うサンプル

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

sourceCompatibility = '1.7'
targetCompatibility = '1.7'

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

repositories {
    mavenCentral()
}

// Eclipse Link を使って JPA の canonical metamodel クラスを生成する Annotation Processing のサンプル

dependencies {
    compile 'org.eclipse.persistence:org.eclipse.persistence.jpa:2.5.+'
    // Annotation Processor を含むライブラリ
    apt     'org.eclipse.persistence:org.eclipse.persistence.jpa.modelgen.processor:2.5.+'
}

procJava {
    // ここでは EclipseLink の実装を使って JPA の canonical metamodel クラスを生成する

    def persistencexml = new File(project.projectDir, 'src/main/resources/META-INF/persistence.xml').absolutePath
    // 処理対象ソースコードの指定
    source    = project.compileJava.source
    // Annotation Processor の指定
    processor = 'org.eclipse.persistence.internal.jpa.modelgen.CanonicalModelProcessor'
    // `javac` コマンドの `-A` オプションに渡す値
    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

class JavaAPT extends DefaultTask {
    private File _destinationDir
    def getDestinationDir(dir) { _destinationDir }
    void setDestinationDir(dir) {
        _destinationDir = dir
        outputs.dir _destinationDir
    }

    private Object _source
    def getSource() { _source }
    void setSource(src) {
        _source = src
        inputs.source src
    }

    String processor
    String apOptions

    @TaskAction
    void process() {
        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 aptTarget = 'src/main/javaGen'
            project.tasks.compileJava.dependsOn it
            project.sourceSets.main.java.srcDirs << aptTarget
            destinationDir = new File(project.projectDir, aptTarget)
        }
        project.configurations {
            apt {
                description "for annotation processors"
            }
        }
    }
}

Thanks for the code @nobuoka.
I have forked it, and fixed it for Gradle 4.2, added an option for easy skipping in multi-project build, and added the missing import to the JavaAptPlugin.groovy file.
Fork is here:
https://gist.github.com/istvanszoboszlai/6ae8440a5f8ba818e29bedfd68bbce2d