have you tried writing a task for it in your build.gradle?
task obfuscate(type: proguard.gradle.ProGuardTask, dependsOn: jar) {
mustRunAfter ('javadoc')
inputs.file file("${jar.archivePath}")
outputs.file file("$buildDir/proguard/${project.name}-${project.version}.jar")
injars "${jar.archivePath}"
// JDK 8 and below use jars on the classpath
if (JavaVersion.current().java8Compatible && !JavaVersion.current().java9Compatible) {
println "Obfuscation inputs based on JDK 8 layout."
libraryjars "$javaHome/lib/rt.jar"
libraryjars "$javaHome/lib/jce.jar"
libraryjars "$javaHome/lib/ext/jfxrt.jar"
} else {
// JDK 9 and above use modules on the module-path
println "Obfuscation inputs based on JDK 9+ module layout."
def jdkModuleList = [
'java.base', 'java.datatransfer', 'java.desktop',
'java.instrument', 'java.logging',
'java.management', 'java.prefs', 'java.rmi',
'java.scripting', 'java.xml',
'jdk.attach'
]
jdkModuleList.forEach {
libraryjars "$javaHome/jmods/${it}.jmod", jarfilter: '!**.jar', filter: '!module-info.class'
}
target '10' // JDK 9 is obsolete, would target 11, but Proguard can't deal with 11's class files yet
}
// dependencies
configurations.runtime.files.each {
libraryjars it, filter: '!META-INF/versions/**'
}
outjars "$buildDir/proguard/${project.name}-${project.version}.jar"
printseeds "$buildDir/proguard/proguard_seeds.txt"
printmapping "$buildDir/proguard/proguard_map.txt"
configuration 'src/main/proguard/configuration.pro'
}
this thread might be helpful with your situation:
https://discuss.gradle.org/t/obfuscated-jars-what-are-the-best-practices/18834/6