upgrade to nextflow 25.10.0

Signed-off-by: Jorge Aguilera <[email protected]>

Author: jagedn

build.gradle

@@ -33,7 +33,7 @@ antora {
 }
 
 nextflowPlugin {
-    nextflowVersion = '24.10.4'
+    nextflowVersion = '25.10.0'
     description = 'An Hashicorp Nomad executor plugin'
     provider = 'nextflow-io'
     className = 'nextflow.nomad.NomadPlugin'

gradle.properties

@@ -1,2 +1,2 @@
-version= 0.4.0-edge1
-github_organization=nextflow-io
+version= 0.4.0-edge2
+github_organization=nextflow-io

src/main/groovy/nextflow/nomad/NomadPlugin.groovy

@@ -23,8 +23,7 @@ import nextflow.cli.PluginAbstractExec
 import nextflow.nomad.secrets.NomadSecretCmd
 import nextflow.nomad.executor.TaskDirectives
 import nextflow.plugin.BasePlugin
-import nextflow.script.ProcessConfig
-import nextflow.secret.SecretsLoader
+import nextflow.script.dsl.ProcessBuilder
 import org.pf4j.PluginWrapper
 
 /**
@@ -40,11 +39,10 @@ class NomadPlugin extends BasePlugin implements PluginAbstractExec{
     NomadPlugin(PluginWrapper wrapper) {
         super(wrapper)
         addCustomDirectives()
-        SecretsLoader.instance.reset()
     }
 
     private static void addCustomDirectives() {
-        ProcessConfig.DIRECTIVES.addAll(TaskDirectives.ALL)
+        ProcessBuilder.DIRECTIVES.addAll(TaskDirectives.ALL)
     }
 
     @Override

src/main/groovy/nextflow/nomad/executor/NomadExecutor.groovy

@@ -40,7 +40,7 @@ import org.pf4j.ExtensionPoint
 class NomadExecutor extends Executor implements ExtensionPoint {
 
     private NomadService service
-    private NomadConfig config
+    private NomadConfig nomadConfig
 
     @Override
     protected void register() {
@@ -49,21 +49,21 @@ class NomadExecutor extends Executor implements ExtensionPoint {
     }
 
     protected void initNomadService(){
-        this.config = new NomadConfig((session.config.nomad ?: Collections.emptyMap()) as Map)
-        this.service = new NomadService(this.config)
+        this.nomadConfig = new NomadConfig((session.config.nomad ?: Collections.emptyMap()) as Map)
+        this.service = new NomadService(this.nomadConfig)
     }
 
     @Override
     protected TaskMonitor createTaskMonitor() {
-        TaskPollingMonitor.create(session, name, 100, Duration.of('5 sec'))
+        TaskPollingMonitor.create(session, config, name, Duration.of('5 sec'))
     }
 
     @Override
     TaskHandler createTaskHandler(TaskRun task) {
         assert task
         assert task.workDir
         log.trace "[NOMAD] launching process > ${task.name} -- work folder: ${task.workDirStr}"
-        return new NomadTaskHandler(task, this.config, service)
+        return new NomadTaskHandler(task, this.nomadConfig, service)
     }
 
     @Override

src/main/groovy/nextflow/nomad/executor/NomadTaskHandler.groovy

@@ -149,9 +149,15 @@ class NomadTaskHandler extends TaskHandler implements FusionAwareTask {
 
     @Override
     void kill() {
+        super.kill()
         nomadService.kill(this.jobName)
     }
 
+    @Override
+    void killTask(){
+        kill()
+    }
+
     @Override
     void submit() {
         submitTask()

src/main/groovy/nextflow/nomad/secrets/NomadSecretProvider.groovy

@@ -38,6 +38,9 @@ class NomadSecretProvider extends LocalSecretsProvider implements SecretsProvide
 
     protected boolean isEnabled(){
         if( !config ){
+            if( !Global.config ){
+                return false
+            }
             config = new NomadConfig(Global.config?.nomad as Map ?: Map.of())
         }
         config?.jobOpts()?.secretOpts?.enabled

validation/run-pipeline.sh

@@ -6,4 +6,4 @@
 
 NXF_ASSETS=$(pwd)/nomad_temp/scratchdir/assets \
   NXF_CACHE_DIR=$(pwd)/nomad_temp/scratchdir/cache \
-    nextflow run -w $(pwd)/nomad_temp/scratchdir/ "$@"
+    nextflow ${REMOTE_DEBUG} run -w $(pwd)/nomad_temp/scratchdir/ "$@"