feat: Add extension point interfaces for standalone plugin development

- Add PluginExtensionPoint base interface for all plugin extensions
- Add Factory annotation for channel factory extensions
- Add Function annotation for custom function extensions
- Add Operator annotation for channel operator extensions
- Add CommandExtensionPoint interface for first-class CLI commands

These interfaces enable standalone plugin development by providing
compile-time access to Nextflow extension points without requiring
the full Nextflow runtime as a dependency.

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <[email protected]>

Author: edmundmiller

src/main/groovy/io/nextflow/gradle/extensions/CommandExtensionPoint.groovy

@@ -0,0 +1,72 @@
+/*
+ * Copyright 2013-2024, 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 io.nextflow.gradle.extensions
+
+import org.pf4j.ExtensionPoint
+
+/**
+ * Extension point interface for plugins that want to register top-level CLI commands.
+ * 
+ * Plugins implementing this interface can provide commands that appear as first-class
+ * citizens in the Nextflow CLI, accessible directly as 'nextflow <command>' rather than
+ * through the legacy 'nextflow plugin <pluginId>:<command>' syntax.
+ * 
+ * Example:
+ * - Instead of: nextflow plugin nf-wave:get-container
+ * - Enable: nextflow wave get-container
+ *
+ * @author Edmund Miller <[email protected]>
+ */
+interface CommandExtensionPoint extends ExtensionPoint {
+
+    /**
+     * Get the primary command name that this plugin registers.
+     * This will be the top-level command name (e.g., "wave", "launch").
+     *
+     * @return The command name that will be available at the top level
+     */
+    String getCommandName()
+
+    /**
+     * Get the command description for help output.
+     * This description will appear in the main help listing.
+     *
+     * @return A brief description of what this command does
+     */
+    String getCommandDescription()
+
+    /**
+     * Get the priority for this command extension.
+     * Higher priority commands will take precedence in case of name conflicts.
+     * Built-in commands have priority 1000 by default.
+     *
+     * @return Priority value (higher = higher priority), defaults to 100
+     */
+    default int getPriority() { return 100 }
+
+    /**
+     * Create the actual command instance that will handle execution.
+     * This method is called when the command needs to be instantiated.
+     *
+     * Note: This returns Object to avoid coupling the gradle plugin to Nextflow's CmdBase.
+     * Implementations should return a nextflow.cli.CmdBase instance.
+     *
+     * @return A CmdBase instance that will handle the command execution
+     */
+    Object createCommand()
+
+}

src/main/groovy/io/nextflow/gradle/extensions/Factory.groovy

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+/*
+ * Copyright 2013-2024, 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 io.nextflow.gradle.extensions
+
+/**
+ * An annotation interface for channel factories that the plugin want to expose
+ * Nextflow will search for all methods annotated with @Factory in the ExtensionPoint and allow to the user imported them
+ *
+ * @author : jorge <[email protected]>
+ *
+ */
+import java.lang.annotation.ElementType
+import java.lang.annotation.Retention
+import java.lang.annotation.RetentionPolicy
+import java.lang.annotation.Target
+
+@Retention(RetentionPolicy.RUNTIME)
+@Target([ElementType.METHOD])
+@interface Factory {
+
+}

src/main/groovy/io/nextflow/gradle/extensions/Function.groovy

@@ -0,0 +1,36 @@
+/*
+ * Copyright 2013-2024, 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 io.nextflow.gradle.extensions
+
+/**
+ * An annotation interface for functions that the plugin want to expose
+ * Nextflow will search for all methods annotated with @Functions in the ExtensionPoint and allow to the user imported them
+ *
+ * @author : jorge <[email protected]>
+ *
+ */
+import java.lang.annotation.ElementType
+import java.lang.annotation.Retention
+import java.lang.annotation.RetentionPolicy
+import java.lang.annotation.Target
+
+@Retention(RetentionPolicy.RUNTIME)
+@Target([ElementType.METHOD])
+@interface Function {
+
+}

src/main/groovy/io/nextflow/gradle/extensions/Operator.groovy

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+/*
+ * Copyright 2013-2024, 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 io.nextflow.gradle.extensions
+
+/**
+ * An annotation interface for operators that the plugin want to expose
+ * Nextflow will search for all methods annotated with @Operators in the ExtensionPoint and allow to the user imported them
+ *
+ * @author : jorge <[email protected]>
+ *
+ */
+import java.lang.annotation.ElementType
+import java.lang.annotation.Retention
+import java.lang.annotation.RetentionPolicy
+import java.lang.annotation.Target
+
+@Retention(RetentionPolicy.RUNTIME)
+@Target([ElementType.METHOD])
+@interface Operator {
+
+}

src/main/groovy/io/nextflow/gradle/extensions/PluginExtensionPoint.groovy

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+/*
+ * Copyright 2013-2024, 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 io.nextflow.gradle.extensions
+
+import groovy.transform.PackageScope
+import org.pf4j.ExtensionPoint
+
+/**
+ * Define plugin extension points. A plugin can provide extension methods
+ * to add custom channel factories, channel operators and custom function
+ * in the including context.
+ *
+ * The extending subclass should mark the extension methods with the
+ * corresponding annotation {@link Factory}, {@link Operator} and {@link Function}
+ *
+ * Note: This returns Object for session to avoid coupling the gradle plugin 
+ * to Nextflow's internal Session class. Implementations should expect a 
+ * nextflow.Session instance.
+ *
+ * @author Paolo Di Tommaso <[email protected]>
+ */
+abstract class PluginExtensionPoint implements ExtensionPoint {
+
+    private boolean initialised
+
+    synchronized void checkInit(Object session) {
+        if( !initialised ) {
+            init(session)
+            initialised = true
+        }
+    }
+
+    /**
+     * Channel factory initialization. This method is invoked one and only once before
+     * the before target extension method is called.
+     *
+     * @param session The current nextflow Session (passed as Object to avoid coupling)
+     */
+    abstract protected void init(Object session)
+
+}