From e1d50218facfec6ffcba0186b82b0d033b2e4350 Mon Sep 17 00:00:00 2001
From: Till Englert <till.englert96@gmail.com>
Date: Mon, 30 Sep 2024 10:58:51 +0200
Subject: [PATCH] Compability with latest stable: nextflow:v24.04.4

---
 .github/workflows/build.yml                       | 10 +++++-----
 Makefile                                          |  7 +++++++
 .../co2footprint/CO2FootprintDslTest.groovy       | 15 +++++++++++++--
 3 files changed, 25 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index 939121b..8b35a52 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -17,23 +17,24 @@ 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
@@ -41,5 +42,4 @@ jobs:
       - name: Tests
         run: ./gradlew check
         env:
-          GRADLE_OPTS: '-Dorg.gradle.daemon=false'
-
+          GRADLE_OPTS: '-Dorg.gradle.daemon=false'
\ No newline at end of file
diff --git a/Makefile b/Makefile
index e6fdc54..de439a7 100644
--- a/Makefile
+++ b/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}
diff --git a/plugins/nf-co2footprint/src/test/nextflow/co2footprint/CO2FootprintDslTest.groovy b/plugins/nf-co2footprint/src/test/nextflow/co2footprint/CO2FootprintDslTest.groovy
index d0d1dcd..943130e 100644
--- a/plugins/nf-co2footprint/src/test/nextflow/co2footprint/CO2FootprintDslTest.groovy
+++ b/plugins/nf-co2footprint/src/test/nextflow/co2footprint/CO2FootprintDslTest.groovy
@@ -1,5 +1,8 @@
 package nextflow.co2footprint
 
+import java.nio.file.Files
+import java.util.jar.Manifest
+
 import nextflow.Channel
 import nextflow.plugin.Plugins
 import nextflow.plugin.TestPluginDescriptorFinder
@@ -36,8 +39,16 @@ class CO2FootprintDslTest extends Dsl2Spec{
             protected PluginDescriptorFinder createPluginDescriptorFinder() {
                 return new TestPluginDescriptorFinder(){
                     @Override
-                    protected Path getManifestPath(Path pluginPath) {
-                        return pluginPath.resolve('build/resources/main/META-INF/MANIFEST.MF')
+                    protected Manifest readManifestFromDirectory(Path pluginPath) {
+                        if( !Files.isDirectory(pluginPath) )
+                            return null
+
+                        final manifestPath = pluginPath.resolve('build/resources/main/META-INF/MANIFEST.MF')
+                        if( !Files.exists(manifestPath) )
+                            return null
+
+                        final input = Files.newInputStream(manifestPath)
+                        return new Manifest(input)
                     }
                 }
             }