Merge branch 'master' into feature/github-actions-release-job

Author: pditommaso

.github/workflows/build.yml

@@ -43,14 +43,14 @@ jobs:
                 COMMIT_MESSAGE="$(curl -s \
                   -H "Authorization: token ${{ secrets.GITHUB_TOKEN }}" \
                   https://api.github.com/repos/${{ github.repository }}/commits/$COMMIT_SHA | jq -r '.commit.message' | head -n 1)"
-                echo "Commit message=$(printf "%q" "$COMMIT_MESSAGE")"
-                echo "commit_message=$(printf "%q" "$COMMIT_MESSAGE")" >> $GITHUB_OUTPUT
+                echo "Commit message=$(printf "%s" "$COMMIT_MESSAGE")"
+                echo "commit_message=$(printf "%s" "$COMMIT_MESSAGE")" >> $GITHUB_OUTPUT
             else
                 echo "GitHub event=${{ github.event_name }}"
                 # Extract only the first line of the commit message
                 COMMIT_MESSAGE="$(git log -1 --pretty=format:'%s')"
-                echo "Commit message=$(printf "%q" "$COMMIT_MESSAGE")"
-                echo "commit_message=$(printf "%q" "$COMMIT_MESSAGE")" >> $GITHUB_OUTPUT
+                echo "Commit message=$(printf "%s" "$COMMIT_MESSAGE")"
+                echo "commit_message=$(printf "%s" "$COMMIT_MESSAGE")" >> $GITHUB_OUTPUT
             fi
 
       - name: Setup env

build.gradle

@@ -100,6 +100,9 @@ allprojects {
             module("commons-logging:commons-logging") { replacedBy("org.slf4j:jcl-over-slf4j") }
         }
 
+        // JUnit Platform launcher required for Gradle 9.1+ when using useJUnitPlatform()
+        testRuntimeOnly 'org.junit.platform:junit-platform-launcher'
+
         // Documentation required libraries
         groovyDoc 'org.fusesource.jansi:jansi:2.4.0'
         groovyDoc "org.apache.groovy:groovy-groovydoc:4.0.28"
@@ -250,20 +253,43 @@ def getRuntimeConfigs() {
         // note: migrating to gradle 7 does not work any more
         //result = result + cfg.getOutgoing().getArtifacts().getFiles()
     }
-    return result
+    return result?.files ?: []
 }
 
 /*
  * Save the runtime classpath
+ * NOTE: This task uses a provider to delay execution, but still triggers configuration
+ * resolution when the provider is evaluated. While not ideal for Gradle 9.1's strict
+ * configuration resolution requirements, this approach works in practice for our use case.
  */
 task exportClasspath {
     dependsOn allprojects.jar
+    
+    // Use provider to delay configuration resolution until task execution
+    def configurationFiles = provider {
+        def libs = []
+        
+        // Resolve configurations during provider evaluation (not ideal but functional)
+        ['nextflow','nf-commons','nf-httpfs','nf-lang','nf-lineage'].each { moduleName ->
+            def moduleProject = project(":$moduleName")
+            def cfg = moduleProject.configurations.getByName('runtimeClasspath')
+            libs.addAll(cfg.files.collect { it.canonicalPath })
+        }
+        
+        // Add module jars
+        ['nextflow','nf-commons','nf-httpfs','nf-lang','nf-lineage'].each {
+            libs << file("modules/$it/build/libs/${it}-${version}.jar").canonicalPath
+        }
+        
+        return libs.unique()
+    }
+    
+    inputs.files(configurationFiles)
+    outputs.file('.launch.classpath')
+    
     doLast {
-        def home = System.getProperty('user.home')
-        def all = getRuntimeConfigs()
-        def libs = all.collect { File file ->  /*println file.canonicalPath.replace(home, '$HOME');*/ file.canonicalPath;  }
-        ['nextflow','nf-commons','nf-httpfs','nf-lang','nf-lineage'].each {libs << file("modules/$it/build/libs/${it}-${version}.jar").canonicalPath }
-        file('.launch.classpath').text = libs.unique().join(':')
+        def libs = configurationFiles.get()
+        file('.launch.classpath').text = libs.join(':')
     }
 }
 

docs/install.md

@@ -12,7 +12,7 @@ New versions of Nextflow are released regularly. See {ref}`updating-nextflow-pag
 
 ## Requirements
 
-Nextflow requires Bash 3.2 (or later) and [Java 17 (or later, up to 24)](http://www.oracle.com/technetwork/java/javase/downloads/index.html) to be installed. To see which version of Java you have, run the following command:
+Nextflow requires Bash 3.2 (or later) and [Java 17 (or later, up to 25)](http://www.oracle.com/technetwork/java/javase/downloads/index.html) to be installed. To see which version of Java you have, run the following command:
 
 ```{code-block} bash
 :class: copyable

gradle/wrapper/gradle-wrapper.jar

@@ -1,6 +1,6 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.14-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-9.1.0-bin.zip
 networkTimeout=10000
 validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME

gradle/wrapper/gradle-wrapper.properties

@@ -66,14 +66,14 @@ fi
 JAVA_VER=$(echo "$JAVA_VER" | awk '/version/ {gsub(/"/, "", $3); print $3}')
 major=${BASH_REMATCH[1]}
 minor=${BASH_REMATCH[2]}
-version_check="^(17|18|19|20|21|23|24)"
+version_check="^(17|18|19|20|21|23|24|25)"
 if [[ ! $JAVA_VER =~ $version_check ]]; then
     echo "Error: cannot find Java or it's a wrong version -- please make sure that Java 17 or higher is installed"
     exit 1
 fi
 JVM_ARGS+=" -Dfile.encoding=UTF-8 -XX:+TieredCompilation -XX:TieredStopAtLevel=1"
 JVM_ARGS+=" --add-opens=java.base/java.lang=ALL-UNNAMED --add-opens=java.base/java.io=ALL-UNNAMED --add-opens=java.base/java.nio=ALL-UNNAMED --add-opens=java.base/java.net=ALL-UNNAMED --add-opens=java.base/java.nio.file.spi=ALL-UNNAMED --add-opens=java.base/java.util=ALL-UNNAMED --add-opens=java.base/java.util.concurrent.locks=ALL-UNNAMED --add-opens=java.base/java.util.concurrent.atomic=ALL-UNNAMED --add-opens=java.base/sun.nio.ch=ALL-UNNAMED --add-opens=java.base/sun.nio.fs=ALL-UNNAMED --add-opens=java.base/sun.net.www.protocol.http=ALL-UNNAMED --add-opens=java.base/sun.net.www.protocol.https=ALL-UNNAMED --add-opens=java.base/sun.net.www.protocol.ftp=ALL-UNNAMED --add-opens=java.base/sun.net.www.protocol.file=ALL-UNNAMED --add-opens=java.base/jdk.internal.misc=ALL-UNNAMED --add-opens=java.base/jdk.internal.vm=ALL-UNNAMED --add-opens=java.base/java.util.regex=ALL-UNNAMED"
-[[ "$JAVA_VER" =~ ^(24) ]]&& JVM_ARGS+=" --enable-native-access=ALL-UNNAMED --sun-misc-unsafe-memory-access=allow"
+[[ "$JAVA_VER" =~ ^(24|25) ]]&& JVM_ARGS+=" --enable-native-access=ALL-UNNAMED --sun-misc-unsafe-memory-access=allow"
 [[ $NXF_ENABLE_VIRTUAL_THREADS == 'true' ]] && [[ "$JAVA_VER" =~ ^(19|20) ]] && JVM_ARGS+=" --enable-preview"
 [[ "$JAVA_VER" =~ ^(21) ]] && [[ ! "$NXF_ENABLE_VIRTUAL_THREADS" ]] && NXF_ENABLE_VIRTUAL_THREADS=true
 

gradlew

@@ -1,5 +1,5 @@
 plugins {
-    id "com.gradleup.shadow" version "8.3.5"
+    id "com.gradleup.shadow" version "8.3.8"
 }
 apply plugin: 'groovy'
 apply plugin: 'application'
@@ -87,11 +87,12 @@ shadowJar {
     configurations = [project.configurations.runtimeClasspath, project.configurations.lineageImplementation]
     archiveClassifier='one'
     manifest {
-        attributes 'Main-Class': "$mainClassName"
+        attributes 'Main-Class': application.mainClass.get()
     }
     mergeServiceFiles()
     mergeGroovyExtensionModules()
     transform(com.github.jengelman.gradle.plugins.shadow.transformers.AppendingTransformer) {
         resource = 'META-INF/extensions.idx'
     }
 }
+

gradlew.bat

@@ -256,7 +256,7 @@ class ScriptMeta {
         final result = new HashSet(definitions.size() + imports.size())
         // local definitions
         for( def item : definitions.values() ) {
-            if( item instanceof WorkflowDef )
+            if( item instanceof WorkflowDef && item.name )
                 result.add(item.name)
         }
         // processes from imports