Align to latest Nextflow version and bump to groovy 4.0

.github/workflows/build.yml

@@ -17,29 +17,29 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        java_version: [8, 11]
+        java_version: [11, 21]
 
     steps:
       - name: Environment
         run: env | sort
 
       - name: Checkout
-        uses: actions/checkout@v1
+        uses: actions/checkout@v3
         with:
           fetch-depth: 1
           submodules: true
 
       - name: Setup Java ${{ matrix.java_version }}
-        uses: actions/setup-java@v1
+        uses: actions/setup-java@v3
         with:
           java-version: ${{matrix.java_version}}
           architecture: x64
+          distribution: 'temurin'
 
       - name: Compile
         run: ./gradlew assemble
 
       - name: Tests
         run: ./gradlew check
         env:
-          GRADLE_OPTS: '-Dorg.gradle.daemon=false'
-
+          GRADLE_OPTS: '-Dorg.gradle.daemon=false'

Makefile

@@ -12,6 +12,10 @@ NXF_HOME ?= $$HOME/.nextflow
 NXF_PLUGINS_DIR ?= $(NXF_HOME)/plugins
 
 clean:
+	rm -rf .nextflow*
+	rm -rf work
+	rm -rf build
+	rm -rf plugins/*/build
 	./gradlew clean
 
 compile:
@@ -48,6 +52,9 @@ else
 	./gradlew ${mm}test --tests ${class}
 endif
 
+assemble:
+	./gradlew assemble
+
 install:
 	./gradlew copyPluginZip
 	rm -rf ${NXF_PLUGINS_DIR}/nf-co2footprint-${version}

gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,7 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-7.3.3-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.9-bin.zip
+networkTimeout=10000
+validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists