use the nextflow gradle plugin

Author: nvnieuwk

.github/workflows/build-docs.yml

@@ -19,7 +19,7 @@ jobs:
           python-version: 3.x
       - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV
       - name: Obtain version from MANIFEST.MF
-        run: echo "plugin_version=$(grep "Plugin-Version" plugins/nf-schema/src/resources/META-INF/MANIFEST.MF | awk '{print $2}' | awk -F '.' '{print $1"."$2}')" >> $GITHUB_ENV
+        run: echo "plugin_version=$(grep "version = " build.gradle | sed -e 's/version = //' | cut -d "'" -f 2)" >> $GITHUB_ENV
       - name: Setup git user
         run: |
           git config --global user.name "${{github.actor}}"

Makefile

@@ -1,65 +1,23 @@
-
-config ?= compileClasspath
-version ?= $(shell grep 'Plugin-Version' plugins/nf-schema/src/resources/META-INF/MANIFEST.MF | awk '{ print $$2 }')
-
-ifdef module 
-mm = :${module}:
-else 
-mm = 
-endif 
+# Build the plugin
+assemble:
+	./gradlew assemble
 
 clean:
+	rm -rf .nextflow*
+	rm -rf work
+	rm -rf build
 	./gradlew clean
 
-compile:
-	./gradlew compileGroovy
-	@echo "DONE `date`"
-
-
-check:
-	./gradlew check
-
-
-#
-# Show dependencies try `make deps config=runtime`, `make deps config=google`
-#
-deps:
-	./gradlew -q ${mm}dependencies --configuration ${config}
-
-deps-all:
-	./gradlew -q dependencyInsight --configuration ${config} --dependency ${module}
-
-#
-# Refresh SNAPSHOTs dependencies
-#
-refresh:
-	./gradlew --refresh-dependencies 
-
 #
 # Run all tests or selected ones
 #
 test:
-ifndef class
-	./gradlew ${mm}test
-else
-	./gradlew ${mm}test --tests ${class}
-endif
-
+	./gradlew test
 
+# Install the plugin into local nextflow plugins dir
 install:
-	./gradlew copyPluginZip
-	rm -rf ${HOME}/.nextflow/plugins/nf-schema-${version}
-	cp -r build/plugins/nf-schema-${version} ${HOME}/.nextflow/plugins/nf-schema-${version}
-
-#
-# Upload JAR artifacts to Maven Central
-#
-upload:
-	./gradlew upload
-
-
-upload-plugins:
-	./gradlew plugins:upload
+	./gradlew install
 
-publish-index:
-	./gradlew plugins:publishIndex
+# Publish the plugin
+release:
+	./gradlew releasePlugin

build.gradle

@@ -0,0 +1,33 @@
+plugins {
+    id 'io.nextflow.nextflow-plugin' version '0.0.1-alpha2'
+}
+
+dependencies {
+    implementation 'org.json:json:20240303'
+    implementation 'dev.harrel:json-schema:1.5.0'
+    implementation 'com.sanctionco.jmail:jmail:1.6.3' // Needed for e-mail format validation
+}
+
+version = '2.4.0dev'
+
+nextflowPlugin {
+    nextflowVersion = '24.10.0'
+
+    provider = 'nextflow'
+    className = 'nextflow.validation.ValidationPlugin'
+    extensionPoints = [
+        'nextflow.validation.ValidationExtension',
+        'nextflow.validation.ValidationObserverFactory'
+    ]
+
+    publishing {
+        github {
+            repository = 'nextflow-io/nf-schema'
+            userName = project.findProperty('github_username')
+            authToken = project.findProperty('github_access_token')
+            email = project.findProperty('github_commit_email')
+
+            indexUrl = 'https://github.com/nextflow-io/plugins/blob/main/plugins.json'
+        }
+    }
+}

docs/contributing/setup.md

@@ -1,5 +1,7 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
 distributionUrl=https\://services.gradle.org/distributions/gradle-8.13-bin.zip
+networkTimeout=10000
+validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

gradle/wrapper/gradle-wrapper.properties

@@ -8,5 +8,3 @@
  */
 
 rootProject.name = 'nf-schema'
-include 'plugins'
-include('plugins:nf-schema')