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Add useDefaultDependencies configuration option
- Add useDefaultDependencies boolean property to NextflowPluginConfig (defaults to true) - Refactor dependency management in NextflowPlugin to use addDefaultDependencies method - Add comprehensive unit tests for the new configuration option - Update README with detailed documentation of default dependencies and usage examples 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]>
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‎README.md‎

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@@ -48,6 +48,7 @@ The `nextflowPlugin` block supports the following configuration options:
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- **`description`** (optional) - A short description of the plugin
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- **`requirePlugins`** (optional) - List of plugin dependencies that must be present
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- **`extensionPoints`** (optional) - List of extension point class names provided by the plugin
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- **`useDefaultDependencies`** (optional, default: `true`) - Whether to automatically add default dependencies required for Nextflow plugin development
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### Registry Configuration
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@@ -92,6 +93,50 @@ You should also ensure that your project's `settings.gradle` declares the plugin
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rootProject.name = '<YOUR-PLUGIN-NAME>'
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```
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### Default Dependencies
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By default, the plugin automatically adds several dependencies required for Nextflow plugin development. You can disable this behavior by setting `useDefaultDependencies = false` in your plugin configuration.
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When `useDefaultDependencies` is `true` (default), the following dependencies are automatically added:
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**Compile-time dependencies (compileOnly):**
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- `io.nextflow:nextflow:${nextflowVersion}` - Core Nextflow classes
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- `org.slf4j:slf4j-api:1.7.10` - Logging API
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- `org.pf4j:pf4j:3.4.1` - Plugin framework
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**Test dependencies (testImplementation):**
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- `org.apache.groovy:groovy` - Groovy language support
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- `io.nextflow:nextflow:${nextflowVersion}` - Nextflow runtime for testing
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- `org.spockframework:spock-core:2.3-groovy-4.0` - Spock testing framework
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- `org.spockframework:spock-junit4:2.3-groovy-4.0` - Spock JUnit4 integration
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**Test runtime dependencies:**
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- `org.objenesis:objenesis:3.4` - Object instantiation library
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- `net.bytebuddy:byte-buddy:1.14.17` - Code generation library
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**Test fixtures:**
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- `testFixtures("io.nextflow:nextflow:${nextflowVersion}")` - Nextflow test utilities
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- `testFixtures("io.nextflow:nf-commons:${nextflowVersion}")` - Common test utilities
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To disable default dependencies and manage them manually:
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```gradle
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nextflowPlugin {
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nextflowVersion = '25.04.0'
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provider = 'Example Inc'
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className = 'com.example.ExamplePlugin'
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useDefaultDependencies = false
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// Add your own dependencies in the dependencies block
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}
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dependencies {
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// Your custom dependencies here
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compileOnly 'io.nextflow:nextflow:25.04.0'
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// etc...
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}
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```
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## Migrating an existing Nextflow plugin
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Follow these steps to migrate an existing Nextflow plugin:

‎src/main/groovy/io/nextflow/gradle/NextflowPlugin.groovy‎

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@@ -62,30 +62,8 @@ class NextflowPlugin implements Plugin<Project> {
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config.validate()
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final nextflowVersion = config.nextflowVersion
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project.dependencies { deps ->
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// required compile-time dependencies for nextflow plugins
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deps.compileOnly "io.nextflow:nextflow:${nextflowVersion}"
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deps.compileOnly "org.slf4j:slf4j-api:1.7.10"
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deps.compileOnly "org.pf4j:pf4j:3.4.1"
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// see https://docs.gradle.org/4.1/userguide/dependency_management.html#sec:module_replacement
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deps.modules {
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module("commons-logging:commons-logging") { replacedBy("org.slf4j:jcl-over-slf4j") }
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}
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// test-only dependencies (for writing tests)
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deps.testImplementation "org.apache.groovy:groovy"
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deps.testImplementation "io.nextflow:nextflow:${nextflowVersion}"
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deps.testImplementation("org.spockframework:spock-core:2.3-groovy-4.0") {
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exclude group: 'org.apache.groovy'
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}
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deps.testImplementation('org.spockframework:spock-junit4:2.3-groovy-4.0') {
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exclude group: 'org.apache.groovy'
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}
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deps.testRuntimeOnly "org.objenesis:objenesis:3.4"
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deps.testRuntimeOnly "net.bytebuddy:byte-buddy:1.14.17"
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deps.testImplementation(testFixtures("io.nextflow:nextflow:${nextflowVersion}"))
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deps.testImplementation(testFixtures("io.nextflow:nf-commons:${nextflowVersion}"))
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if (config.useDefaultDependencies) {
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addDefaultDependencies(project, nextflowVersion)
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}
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}
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// use JUnit 5 platform
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}
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}
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private void addDefaultDependencies(Project project, String nextflowVersion) {
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project.dependencies { deps ->
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// required compile-time dependencies for nextflow plugins
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deps.compileOnly "io.nextflow:nextflow:${nextflowVersion}"
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deps.compileOnly "org.slf4j:slf4j-api:1.7.10"
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deps.compileOnly "org.pf4j:pf4j:3.4.1"
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// see https://docs.gradle.org/4.1/userguide/dependency_management.html#sec:module_replacement
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deps.modules {
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module("commons-logging:commons-logging") { replacedBy("org.slf4j:jcl-over-slf4j") }
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}
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// test-only dependencies (for writing tests)
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deps.testImplementation "org.apache.groovy:groovy"
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deps.testImplementation "io.nextflow:nextflow:${nextflowVersion}"
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deps.testImplementation("org.spockframework:spock-core:2.3-groovy-4.0") {
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exclude group: 'org.apache.groovy'
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}
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deps.testImplementation('org.spockframework:spock-junit4:2.3-groovy-4.0') {
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exclude group: 'org.apache.groovy'
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}
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deps.testRuntimeOnly "org.objenesis:objenesis:3.4"
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deps.testRuntimeOnly "net.bytebuddy:byte-buddy:1.14.17"
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deps.testImplementation(testFixtures("io.nextflow:nextflow:${nextflowVersion}"))
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deps.testImplementation(testFixtures("io.nextflow:nf-commons:${nextflowVersion}"))
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}
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}
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}

‎src/main/groovy/io/nextflow/gradle/NextflowPluginConfig.groovy‎

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@@ -15,6 +15,7 @@ import org.gradle.api.Project
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* nextflowVersion = '25.04.0'
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* publisher = 'nextflow'
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* className = 'com.example.ExamplePlugin'
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* useDefaultDependencies = false // optional, defaults to true
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* extensionPoints = [
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* 'com.example.ExampleFunctions'
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* ]
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*/
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List<String> extensionPoints = []
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/**
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* Whether to automatically add default dependencies (default: true)
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*/
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boolean useDefaultDependencies = true
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/**
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* Configure registry publishing settings (optional)
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*/

‎src/test/groovy/io/nextflow/gradle/NextflowPluginTest.groovy‎

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@@ -154,4 +154,78 @@ class NextflowPluginTest extends Specification {
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project.tasks.findByName('installPlugin') != null
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}
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def "should add default dependencies when useDefaultDependencies is true"() {
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given:
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project.nextflowPlugin {
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description = 'A test plugin'
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provider = 'Test Author'
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className = 'com.example.TestPlugin'
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nextflowVersion = '24.04.0'
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useDefaultDependencies = true
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extensionPoints = ['com.example.TestExtension']
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}
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when:
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project.evaluate()
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then:
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def compileOnlyDeps = project.configurations.compileOnly.dependencies
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compileOnlyDeps.find { it.group == 'io.nextflow' && it.name == 'nextflow' && it.version == '24.04.0' }
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compileOnlyDeps.find { it.group == 'org.slf4j' && it.name == 'slf4j-api' && it.version == '1.7.10' }
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compileOnlyDeps.find { it.group == 'org.pf4j' && it.name == 'pf4j' && it.version == '3.4.1' }
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and: "test dependencies should be added"
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def testDeps = project.configurations.testImplementation.dependencies
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testDeps.find { it.group == 'org.apache.groovy' && it.name == 'groovy' }
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testDeps.find { it.group == 'io.nextflow' && it.name == 'nextflow' && it.version == '24.04.0' }
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testDeps.find { it.group == 'org.spockframework' && it.name == 'spock-core' }
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}
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def "should not add default dependencies when useDefaultDependencies is false"() {
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given:
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project.nextflowPlugin {
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description = 'A test plugin'
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provider = 'Test Author'
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className = 'com.example.TestPlugin'
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nextflowVersion = '24.04.0'
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useDefaultDependencies = false
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extensionPoints = ['com.example.TestExtension']
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}
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when:
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project.evaluate()
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then:
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def compileOnlyDeps = project.configurations.compileOnly.dependencies
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!compileOnlyDeps.find { it.group == 'io.nextflow' && it.name == 'nextflow' }
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!compileOnlyDeps.find { it.group == 'org.slf4j' && it.name == 'slf4j-api' }
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!compileOnlyDeps.find { it.group == 'org.pf4j' && it.name == 'pf4j' }
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and: "test dependencies should not be added"
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def testDeps = project.configurations.testImplementation.dependencies
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!testDeps.find { it.group == 'org.apache.groovy' && it.name == 'groovy' }
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!testDeps.find { it.group == 'io.nextflow' && it.name == 'nextflow' }
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!testDeps.find { it.group == 'org.spockframework' && it.name == 'spock-core' }
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}
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def "should add default dependencies by default when useDefaultDependencies is not specified"() {
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given:
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project.nextflowPlugin {
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description = 'A test plugin'
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provider = 'Test Author'
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className = 'com.example.TestPlugin'
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nextflowVersion = '24.04.0'
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extensionPoints = ['com.example.TestExtension']
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}
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when:
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project.evaluate()
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then:
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def compileOnlyDeps = project.configurations.compileOnly.dependencies
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compileOnlyDeps.find { it.group == 'io.nextflow' && it.name == 'nextflow' && it.version == '24.04.0' }
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compileOnlyDeps.find { it.group == 'org.slf4j' && it.name == 'slf4j-api' && it.version == '1.7.10' }
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compileOnlyDeps.find { it.group == 'org.pf4j' && it.name == 'pf4j' && it.version == '3.4.1' }
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}
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}

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