Merge branch 'master' into nextflow-auth

Author: ewels

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

@@ -15,6 +15,8 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
+# SPDX-License-Identifier: Apache-2.0
+#
 
 ##############################################################################
 #
@@ -84,7 +86,7 @@ done
 # shellcheck disable=SC2034
 APP_BASE_NAME=${0##*/}
 # Discard cd standard output in case $CDPATH is set (https://github.com/gradle/gradle/issues/25036)
-APP_HOME=$( cd "${APP_HOME:-./}" > /dev/null && pwd -P ) || exit
+APP_HOME=$( cd -P "${APP_HOME:-./}" > /dev/null && printf '%s\n' "$PWD" ) || exit
 
 # Use the maximum available, or set MAX_FD != -1 to use that value.
 MAX_FD=maximum
@@ -112,7 +114,7 @@ case "$( uname )" in                #(
   NONSTOP* )        nonstop=true ;;
 esac
 
-CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
+CLASSPATH="\\\"\\\""
 
 
 # Determine the Java command to use to start the JVM.
@@ -203,15 +205,15 @@ fi
 DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
 
 # Collect all arguments for the java command:
-#   * DEFAULT_JVM_OPTS, JAVA_OPTS, JAVA_OPTS, and optsEnvironmentVar are not allowed to contain shell fragments,
+#   * DEFAULT_JVM_OPTS, JAVA_OPTS, and optsEnvironmentVar are not allowed to contain shell fragments,
 #     and any embedded shellness will be escaped.
 #   * For example: A user cannot expect ${Hostname} to be expanded, as it is an environment variable and will be
 #     treated as '${Hostname}' itself on the command line.
 
 set -- \
         "-Dorg.gradle.appname=$APP_BASE_NAME" \
         -classpath "$CLASSPATH" \
-        org.gradle.wrapper.GradleWrapperMain \
+        -jar "$APP_HOME/gradle/wrapper/gradle-wrapper.jar" \
         "$@"
 
 # Stop when "xargs" is not available.

gradlew

@@ -13,6 +13,8 @@
 @rem See the License for the specific language governing permissions and
 @rem limitations under the License.
 @rem
+@rem SPDX-License-Identifier: Apache-2.0
+@rem
 
 @if "%DEBUG%"=="" @echo off
 @rem ##########################################################################
@@ -68,11 +70,11 @@ goto fail
 :execute
 @rem Setup the command line
 
-set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar
+set CLASSPATH=
 
 
 @rem Execute Gradle
-"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %*
+"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" -jar "%APP_HOME%\gradle\wrapper\gradle-wrapper.jar" %*
 
 :end
 @rem End local scope for the variables with windows NT shell

gradlew.bat

@@ -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
 

launch.sh

@@ -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'
     }
 }
+

modules/nextflow/build.gradle

@@ -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 && item.name != null )
+            if( item instanceof WorkflowDef && item.name )
                 result.add(item.name)
         }
         // processes from imports

modules/nextflow/src/main/groovy/nextflow/script/ScriptMeta.groovy

@@ -626,4 +626,22 @@ class ScriptDslTest extends Dsl2Spec {
         e2.message == 'Missing process or function Channel.doesNotExist()'
     }
 
+    def 'should show proper error message for invalid entry name' () {
+        when:
+        // Use dsl_eval with an invalid entry name to trigger the error
+        dsl_eval('invalidEntry', '''
+        workflow validWorkflow {
+          /println 'valid'/
+        }
+        
+        workflow {
+          /println 'default'/
+        }
+        ''')
+        
+        then:
+        def err = thrown(IllegalArgumentException)
+        err.message.contains('Unknown workflow entry name: invalidEntry')
+    }
+
 }