Refactor K8s support as core plug-in (#5965)

Signed-off-by: Paolo Di Tommaso <[email protected]>
Signed-off-by: Ben Sherman <[email protected]>
Co-authored-by: Ben Sherman <[email protected]>

Author: pditommaso

VERSION

@@ -1 +1 @@
-25.02.3-edge
+25.03.0-edge

docs/plugins.md

@@ -14,6 +14,7 @@ The following functionalities are provided via plugin components, and they make
 - `nf-azure`: Support for Microsoft Azure.
 - `nf-cloudcache`: Support for the cloud cache (see `NXF_CLOUDCACHE_PATH` under {ref}`config-env-vars`).
 - `nf-console`: Implement Nextflow [REPL console](https://www.nextflow.io/blog/2015/introducing-nextflow-console.html).
+- `nf-k8s`: Support for Kubernetes.
 - `nf-google`: Support for Google Cloud.
 - `nf-tower`: Support for [Seqera Platform](https://seqera.io) (formerly Tower Cloud).
 - `nf-wave`: Support for [Wave containers](https://seqera.io/wave/) service.

modules/nextflow/build.gradle

@@ -48,8 +48,6 @@ dependencies {
     api 'jline:jline:2.9'
     api 'org.pf4j:pf4j:3.12.0'
     api 'dev.failsafe:failsafe:3.1.0'
-    api 'org.bouncycastle:bcprov-ext-jdk18on:1.78.1'
-    api 'org.bouncycastle:bcpkix-jdk18on:1.78.1'
     api 'io.seqera:lib-trace:0.1.0'
 
     testImplementation 'org.subethamail:subethasmtp:3.1.7'

modules/nextflow/src/main/groovy/nextflow/cli/CmdKubeRun.groovy

@@ -21,7 +21,8 @@ import com.beust.jcommander.Parameters
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
 import nextflow.exception.AbortOperationException
-import nextflow.k8s.K8sDriverLauncher
+import nextflow.plugin.Plugins
+import org.pf4j.ExtensionPoint
 /**
  * Extends `run` command to support Kubernetes deployment
  * 
@@ -32,6 +33,10 @@ import nextflow.k8s.K8sDriverLauncher
 @Parameters(commandDescription = "Execute a workflow in a Kubernetes cluster (experimental)")
 class CmdKubeRun extends CmdRun {
 
+    interface KubeCommand extends ExtensionPoint {
+        int run(CmdKubeRun cmd, String pipeline, List<String> args)
+    }
+
     static private String POD_NAME = /[a-z0-9]([-a-z0-9]*[a-z0-9])?(\.[a-z0-9]([-a-z0-9]*[a-z0-9])?)*/
 
     /**
@@ -76,7 +81,7 @@ class CmdKubeRun extends CmdRun {
         runName = runName.replace('_','-')
     }
 
-    protected boolean background() { launcher.options.background }
+    boolean background() { launcher.options.background }
 
     protected hasAnsiLogFlag() { launcher.options.hasAnsiLogFlag() }
 
@@ -93,9 +98,11 @@ class CmdKubeRun extends CmdRun {
             headImage = podImage
         }
         checkRunName()
-        final driver = new K8sDriverLauncher(cmd: this, runName: runName, headImage: headImage, background: background(), headCpus: headCpus, headMemory: headMemory, headPreScript: headPreScript, plugins: plugins)
-        driver.run(pipeline, scriptArgs)
-        final status = driver.shutdown()
+        Plugins.init()
+        Plugins.start('nf-k8s')
+        // load the command operations
+        final command = Plugins.getExtension(KubeCommand)
+        final status = command.run(this, pipeline, scriptArgs)
         System.exit(status)
     }
 

modules/nextflow/src/main/groovy/nextflow/executor/ExecutorFactory.groovy

@@ -22,7 +22,6 @@ import groovy.transform.PackageScope
 import groovy.util.logging.Slf4j
 import nextflow.Session
 import nextflow.executor.local.LocalExecutor
-import nextflow.k8s.K8sExecutor
 import nextflow.script.BodyDef
 import nextflow.script.ProcessConfig
 import nextflow.script.ScriptType
@@ -57,7 +56,6 @@ class ExecutorFactory {
             'crg': CrgExecutor,
             'bsc': LsfExecutor,
             'condor': CondorExecutor,
-            'k8s': K8sExecutor,
             'nqsii': NqsiiExecutor,
             'moab': MoabExecutor,
             'oar': OarExecutor,

modules/nextflow/src/main/groovy/nextflow/processor/TaskConfig.groovy

@@ -30,7 +30,6 @@ import nextflow.exception.ProcessUnrecoverableException
 import nextflow.executor.BashWrapperBuilder
 import nextflow.executor.res.AcceleratorResource
 import nextflow.executor.res.DiskResource
-import nextflow.k8s.model.PodOptions
 import nextflow.script.TaskClosure
 import nextflow.util.CmdLineHelper
 import nextflow.util.CmdLineOptionMap
@@ -499,10 +498,6 @@ class TaskConfig extends LazyMap implements Cloneable {
         get('retryCount') as Integer ?: 0
     }
 
-    PodOptions getPodOptions() {
-        new PodOptions((List)get('pod'))
-    }
-
     AcceleratorResource getAccelerator() {
         final value = get('accelerator')
         if( value instanceof Number )

modules/nextflow/src/main/resources/META-INF/plugins-info.txt

@@ -4,5 +4,6 @@ [email protected]
 [email protected]
 [email protected]
 [email protected]
+[email protected]
 [email protected]
 [email protected]

modules/nextflow/src/test/groovy/nextflow/executor/ExecutorFactoryTest.groovy

@@ -20,7 +20,6 @@ import nextflow.executor.local.LocalExecutor
 import spock.lang.Specification
 
 import nextflow.Session
-import nextflow.k8s.K8sExecutor
 import nextflow.script.ProcessConfig
 import nextflow.processor.TaskHandler
 import nextflow.processor.TaskMonitor
@@ -50,7 +49,6 @@ class ExecutorFactoryTest extends Specification {
         factory.getExecutorClass('pbs') == PbsExecutor
         factory.getExecutorClass('slurm') == SlurmExecutor
         factory.getExecutorClass('condor') == CondorExecutor
-        factory.getExecutorClass('k8s') == K8sExecutor
         factory.getExecutorClass('x') == XExecutor  // <-- this is loaded by the name
 
         when:

modules/nextflow/src/test/groovy/nextflow/processor/TaskConfigTest.groovy

@@ -15,11 +15,11 @@
  */
 
 package nextflow.processor
+
 import java.nio.file.Paths
 
 import nextflow.exception.FailedGuardException
 import nextflow.exception.ProcessUnrecoverableException
-import nextflow.k8s.model.PodOptions
 import nextflow.script.BaseScript
 import nextflow.script.ProcessConfig
 import nextflow.script.TaskClosure
@@ -545,9 +545,9 @@ class TaskConfigTest extends Specification {
                     [secret: 'foo', mountPath: '/this'],
                     [secret: 'bar', env: 'BAR_XXX'] ]
 
-        process.createTaskConfig().getPodOptions() == new PodOptions([
-                    [secret: 'foo', mountPath: '/this'],
-                    [secret: 'bar', env: 'BAR_XXX'] ])
+        process.createTaskConfig().get('pod') == [
+            [secret: 'foo', mountPath: '/this'],
+            [secret: 'bar', env: 'BAR_XXX'] ]
     }
 
     def 'should get gpu resources' () {

modules/nf-commons/src/main/nextflow/plugin/PluginsFacade.groovy

@@ -416,6 +416,9 @@ class PluginsFacade implements PluginStateListener {
         if( executor == 'azurebatch' || workDir?.startsWith('az://') || bucketDir?.startsWith('az://') )
             plugins << defaultPlugins.getPlugin('nf-azure')
 
+        if( executor == 'k8s' )
+            plugins << defaultPlugins.getPlugin('nf-k8s')
+
         if( Bolts.navigate(config, 'weblog.enabled'))
             plugins << new PluginSpec('nf-weblog')
 

modules/nf-commons/src/test/nextflow/plugin/PluginsFacadeTest.groovy

@@ -183,7 +183,8 @@ class PluginsFacadeTest extends Specification {
                 'nf-amazon': new PluginSpec('nf-amazon', '0.1.0'),
                 'nf-google': new PluginSpec('nf-google', '0.1.0'),
                 'nf-azure': new PluginSpec('nf-azure', '0.1.0'),
-                'nf-tower': new PluginSpec('nf-tower', '0.1.0')
+                'nf-tower': new PluginSpec('nf-tower', '0.1.0'),
+                'nf-k8s': new PluginSpec('nf-k8s', '0.1.0')
         ])
         and:
         def handler = new PluginsFacade(defaultPlugins: defaults)
@@ -210,6 +211,12 @@ class PluginsFacadeTest extends Specification {
         !plugins.find { it.id == 'nf-amazon' }
         plugins.find { it.id == 'nf-azure' }
 
+        when:
+        plugins = handler.defaultPluginsConf([process:[executor: 'k8s']])
+        then:
+        plugins.find { it.id == 'nf-k8s' }
+        !plugins.find { it.id == 'nf-amazon' }
+
         when:
         plugins = handler.defaultPluginsConf([:])
         then:

plugins/nf-k8s/build.gradle

@@ -0,0 +1,50 @@
+/*
+ * Copyright 2019, Google Inc
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+apply plugin: 'java'
+apply plugin: 'java-test-fixtures'
+apply plugin: 'idea'
+apply plugin: 'groovy'
+
+sourceSets {
+    main.java.srcDirs = []
+    main.groovy.srcDirs = ['src/main']
+    main.resources.srcDirs = ['src/resources']
+    test.groovy.srcDirs = ['src/test']
+    test.java.srcDirs = []
+    test.resources.srcDirs = []
+}
+
+configurations {
+    // see https://docs.gradle.org/4.1/userguide/dependency_management.html#sub:exclude_transitive_dependencies
+    runtimeClasspath.exclude group: 'org.slf4j', module: 'slf4j-api'
+}
+
+dependencies {
+    compileOnly project(':nextflow')
+    compileOnly 'org.slf4j:slf4j-api:2.0.16'
+    compileOnly 'org.pf4j:pf4j:3.12.0'
+
+    api 'org.bouncycastle:bcprov-ext-jdk18on:1.78.1'
+    api 'org.bouncycastle:bcpkix-jdk18on:1.78.1'
+
+    testImplementation(testFixtures(project(":nextflow")))
+    testImplementation "org.apache.groovy:groovy:4.0.26"
+    testImplementation "org.apache.groovy:groovy-nio:4.0.26"
+}
+
+test {
+    useJUnitPlatform()
+}

plugins/nf-k8s/changelog.txt

@@ -0,0 +1,4 @@
+nf-k8s changelog
+===================
+1.0.0 - 13 Apr 2025
+- Refactor Kubernetes support as a core plugin

modules/nextflow/src/main/groovy/nextflow/k8s/K8sConfig.groovy renamed to plugins/nf-k8s/src/main/nextflow/k8s/K8sConfig.groovy

@@ -1,5 +1,5 @@
 /*
- * Copyright 2013-2024, Seqera Labs
+ * Copyright 2013-2025, Seqera Labs
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.

modules/nextflow/src/main/groovy/nextflow/k8s/K8sDriverLauncher.groovy renamed to plugins/nf-k8s/src/main/nextflow/k8s/K8sDriverLauncher.groovy

@@ -1,5 +1,5 @@
 /*
- * Copyright 2013-2024, Seqera Labs
+ * Copyright 2013-2025, Seqera Labs
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -38,7 +38,6 @@ import nextflow.k8s.model.PodEnv
 import nextflow.k8s.model.PodMountConfig
 import nextflow.k8s.model.PodSpecBuilder
 import nextflow.k8s.model.ResourceType
-import nextflow.plugin.Plugins
 import nextflow.scm.AssetManager
 import nextflow.scm.ProviderConfig
 import nextflow.util.ConfigHelper
@@ -272,7 +271,6 @@ class K8sDriverLauncher {
 
         if( !interactive && !pipelineName.startsWith('/') && !cmd.remoteProfile && !cmd.runRemoteConfig ) {
             // -- check and parse project remote config
-            Plugins.init()
             final pipelineConfig = new AssetManager(pipelineName, cmd) .getConfigFile()
             builder.setUserConfigFiles(pipelineConfig)
         }

modules/nextflow/src/main/groovy/nextflow/k8s/K8sExecutor.groovy renamed to plugins/nf-k8s/src/main/nextflow/k8s/K8sExecutor.groovy

@@ -1,5 +1,5 @@
 /*
- * Copyright 2013-2024, Seqera Labs
+ * Copyright 2013-2025, Seqera Labs
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -18,7 +18,6 @@ package nextflow.k8s
 
 import groovy.transform.CompileStatic
 import groovy.transform.Memoized
-import groovy.transform.PackageScope
 import groovy.util.logging.Slf4j
 import nextflow.executor.Executor
 import nextflow.fusion.FusionHelper
@@ -29,6 +28,8 @@ import nextflow.processor.TaskPollingMonitor
 import nextflow.processor.TaskRun
 import nextflow.util.Duration
 import nextflow.util.ServiceName
+import org.pf4j.ExtensionPoint
+
 /**
  * Implement the Kubernetes executor
  *
@@ -37,7 +38,7 @@ import nextflow.util.ServiceName
 @Slf4j
 @CompileStatic
 @ServiceName('k8s')
-class K8sExecutor extends Executor {
+class K8sExecutor extends Executor implements ExtensionPoint {
 
     /**
      * The Kubernetes HTTP client

plugins/nf-k8s/src/main/nextflow/k8s/K8sPlugin.groovy

@@ -0,0 +1,34 @@
+/*
+ * Copyright 2013-2025, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package nextflow.k8s
+
+import groovy.transform.CompileStatic
+import nextflow.plugin.BasePlugin
+import org.pf4j.PluginWrapper
+
+/**
+ * Kubernetes plugin entry point
+ *
+ * @author Paolo Di Tommaso <[email protected]>
+ */
+@CompileStatic
+class K8sPlugin extends BasePlugin {
+
+    K8sPlugin(PluginWrapper wrapper) {
+        super(wrapper)
+    }
+}

modules/nextflow/src/main/groovy/nextflow/k8s/K8sTaskHandler.groovy renamed to plugins/nf-k8s/src/main/nextflow/k8s/K8sTaskHandler.groovy

@@ -1,5 +1,5 @@
 /*
- * Copyright 2013-2024, Seqera Labs
+ * Copyright 2013-2025, Seqera Labs
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -276,10 +276,13 @@ class K8sTaskHandler extends TaskHandler implements FusionAwareTask {
         // merge the pod options provided in the k8s config
         // with the ones in process config
         def opt1 = k8sConfig.getPodOptions()
-        def opt2 = task.getConfig().getPodOptions()
+        def opt2 = taskPodOptions()
         return opt1 + opt2
     }
 
+    protected PodOptions taskPodOptions() {
+        new PodOptions((List)task.getConfig().get('pod'))
+    }
 
     protected Map<String,String> getLabels(TaskRun task) {
         final result = new LinkedHashMap<String,String>(10)

modules/nextflow/src/main/groovy/nextflow/k8s/K8sWrapperBuilder.groovy renamed to plugins/nf-k8s/src/main/nextflow/k8s/K8sWrapperBuilder.groovy

@@ -1,5 +1,5 @@
 /*
- * Copyright 2013-2024, Seqera Labs
+ * Copyright 2013-2025, Seqera Labs
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.