Separate CLI from runtime

build.gradle

@@ -325,7 +325,7 @@ task compile {
 
 def getRuntimeConfigs() {
     def names = subprojects
-            .findAll { prj -> prj.name in ['nextflow','nf-commons','nf-httpfs','nf-lang','nf-lineage'] }
+            .findAll { prj -> prj.name in ['nextflow','nf-cli-v1','nf-commons','nf-httpfs','nf-lang','nf-lineage'] }
             .collect { it.name }
 
     FileCollection result = null
@@ -363,7 +363,7 @@ task exportClasspath {
         }
 
         // Add module jars
-        ['nextflow','nf-commons','nf-httpfs','nf-lang','nf-lineage'].each {
+        ['nextflow','nf-cli-v1','nf-commons','nf-httpfs','nf-lang','nf-lineage'].each {
             libs << file("modules/$it/build/libs/${it}-${version}.jar").canonicalPath
         }
 
@@ -387,7 +387,7 @@ ext.nexusEmail = project.findProperty('nexusEmail')
 // `signing.keyId` property needs to be defined in the `gradle.properties` file
 ext.enableSignArchives = project.findProperty('signing.keyId')
 
-ext.coreProjects = projects( ':nextflow', ':nf-commons', ':nf-httpfs', ':nf-lang', ':nf-lineage' )
+ext.coreProjects = projects( ':nextflow', ':nf-cli-v1', ':nf-commons', ':nf-httpfs', ':nf-lang', ':nf-lineage' )
 
 configure(coreProjects) {
     group = 'io.nextflow'

modules/nextflow/build.gradle

@@ -1,8 +1,19 @@
-plugins {
-    id "com.gradleup.shadow" version "8.3.8"
-}
+/*
+ * 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.
+ */
 apply plugin: 'groovy'
-apply plugin: 'application'
 
 sourceSets {
     main.java.srcDirs = []
@@ -13,14 +24,6 @@ sourceSets {
     test.resources.srcDirs = ['src/test/resources']
 }
 
-compileGroovy {
-    options.compilerArgs = ['-XDignore.symbol.file']
-}
-
-configurations {
-    lineageImplementation
-}
-
 dependencies {
     api(project(':nf-commons'))
     api(project(':nf-httpfs'))
@@ -41,14 +44,13 @@ dependencies {
     api "org.apache.commons:commons-lang3:3.18.0"
     api "commons-codec:commons-codec:1.15"
     api "commons-io:commons-io:2.15.1"
-    api "com.beust:jcommander:1.35"
     api("com.esotericsoftware.kryo:kryo:2.24.0") { exclude group: 'com.esotericsoftware.minlog', module: 'minlog' }
-    api('org.iq80.leveldb:leveldb:0.12')
-    api('org.eclipse.jgit:org.eclipse.jgit:7.1.1.202505221757-r')
-    api ('javax.activation:activation:1.1.1')
-    api ('javax.mail:mail:1.4.7')
-    api ('org.yaml:snakeyaml:2.2')
-    api ('org.jsoup:jsoup:1.15.4')
+    api 'org.iq80.leveldb:leveldb:0.12'
+    api 'org.eclipse.jgit:org.eclipse.jgit:7.1.1.202505221757-r'
+    api 'javax.activation:activation:1.1.1'
+    api 'javax.mail:mail:1.4.7'
+    api 'org.yaml:snakeyaml:2.2'
+    api 'org.jsoup:jsoup:1.15.4'
     api 'jline:jline:2.9'
     api 'org.pf4j:pf4j:3.12.0'
     api 'dev.failsafe:failsafe:3.1.0'
@@ -64,36 +66,5 @@ dependencies {
     testFixturesApi ("org.spockframework:spock-core:2.3-groovy-4.0") { exclude group: 'org.apache.groovy' }
     testFixturesApi ('org.spockframework:spock-junit4:2.3-groovy-4.0') { exclude group: 'org.apache.groovy' }
     testFixturesApi 'com.google.jimfs:jimfs:1.2'
-    // note: declare as separate dependency to avoid a circular dependency
-    lineageImplementation (project(':nf-lineage'))
-}
-
-
-test {
-    minHeapSize = "512m"
-    maxHeapSize = "4096m"
-}
-
-application {
-    mainClass = 'nextflow.cli.Launcher'
-}
-
-run{
-    args( (project.hasProperty("runCmd") ? project.findProperty("runCmd") : "set a cmd to run").split(' ') )
-}
-
-shadowJar {
-    // add 'lineage' because it cannot be added to this project
-    // explicitly otherwise it will result into a circular dependency
-    configurations = [project.configurations.runtimeClasspath, project.configurations.lineageImplementation]
-    archiveClassifier='one'
-    manifest {
-        attributes 'Main-Class': application.mainClass.get()
-    }
-    mergeServiceFiles()
-    mergeGroovyExtensionModules()
-    transform(com.github.jengelman.gradle.plugins.shadow.transformers.AppendingTransformer) {
-        resource = 'META-INF/extensions.idx'
-    }
 }
 

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

@@ -0,0 +1,50 @@
+/*
+ * 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.cli
+
+import org.pf4j.ExtensionPoint
+
+/**
+ * Extension point interface for the `auth` command.
+ *
+ * @see io.seqera.tower.plugin.auth.AuthCommandImpl
+ *
+ * @author Phil Ewels <phil.ewels@seqera.io>
+ */
+interface AuthCommand extends ExtensionPoint {
+    /**
+     * Authenticates with Seqera Platform and saves credentials to config.
+     *
+     * @param url the Seqera Platform API endpoint URL (null for default)
+     */
+    void login(String url)
+
+    /**
+     * Revokes access token and removes authentication from local config.
+     */
+    void logout()
+
+    /**
+     * Configures Seqera Platform settings (workspace, monitoring, compute environment).
+     */
+    void config()
+
+    /**
+     * Displays current authentication status and configuration sources.
+     */
+    void status()
+}

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

@@ -0,0 +1,54 @@
+/*
+ * 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.cli
+
+import groovy.transform.CompileStatic
+import org.pf4j.ExtensionPoint
+
+/**
+ * Extension point interface for the `launch` command.
+ *
+ * @see io.seqera.tower.plugin.launch.LaunchCommandImpl
+ *
+ * @author Phil Ewels <phil.ewels@seqera.io>
+ */
+interface LaunchCommand extends ExtensionPoint {
+    void launch(LaunchOptions options)
+}
+
+
+/**
+ * Data class to hold launch options
+ */
+@CompileStatic
+class LaunchOptions {
+    String pipeline
+    String workspace
+    String computeEnv
+    String runName
+    String workDir
+    String revision
+    String profile
+    List<String> configFiles
+    String paramsFile
+    String entryName
+    String resume
+    boolean latest
+    boolean stubRun
+    String mainScript
+    Map<String, String> params
+}