feat: Add package directive to process configuration

Extends process configuration to support the unified package directive:

- ProcessConfig: Adds 'package' to the list of valid directives
- TaskRun: Implements getPackageSpec() method with caching
- TaskBean: Adds packageSpec field for task execution

Also adds deprecation warnings when conda/pixi directives are used
with the preview.package feature enabled, encouraging migration to
the new unified syntax.

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

Co-Authored-By: Claude <[email protected]>
Signed-off-by: Edmund Miller <[email protected]>

Author: edmundmiller

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

@@ -23,6 +23,7 @@ import groovy.transform.PackageScope
 import nextflow.container.ContainerConfig
 import nextflow.executor.BashWrapperBuilder
 import nextflow.executor.TaskArrayExecutor
+import nextflow.packages.PackageSpec
 import nextflow.util.MemoryUnit
 /**
  * Serializable task value object. Holds configuration values required to
@@ -53,6 +54,8 @@ class TaskBean implements Serializable, Cloneable {
 
     Path pixiEnv
 
+    PackageSpec packageSpec
+
     List<String> moduleNames
 
     Path workDir
@@ -141,6 +144,7 @@ class TaskBean implements Serializable, Cloneable {
         this.useMicromamba = task.getCondaConfig()?.useMicromamba()
         this.spackEnv = task.getSpackEnv()
         this.pixiEnv = task.getPixiEnv()
+        this.packageSpec = task.getPackageSpec()
         this.moduleNames = task.config.getModule()
         this.shell = task.config.getShell() ?: BashWrapperBuilder.BASH
         this.script = task.getScript()

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

@@ -54,6 +54,8 @@ import nextflow.script.params.StdInParam
 import nextflow.script.params.ValueOutParam
 import nextflow.pixi.PixiCache
 import nextflow.pixi.PixiConfig
+import nextflow.packages.PackageManager
+import nextflow.packages.PackageSpec
 import nextflow.spack.SpackCache
 /**
  * Models a task instance
@@ -646,6 +648,11 @@ class TaskRun implements Cloneable {
         if( !config.conda || !getCondaConfig().isEnabled() )
             return null
 
+        // Show deprecation warning if new package system is enabled
+        if (PackageManager.isEnabled(processor.session)) {
+            log.warn "The 'conda' directive is deprecated when preview.package is enabled. Use 'package \"${config.conda}\", provider: \"conda\"' instead"
+        }
+
         final cache = new CondaCache(getCondaConfig())
         cache.getCachePathFor(config.conda as String)
     }
@@ -665,6 +672,11 @@ class TaskRun implements Cloneable {
         if( !config.pixi || !processor.session.getPixiConfig().isEnabled() )
             return null
 
+        // Show deprecation warning if new package system is enabled
+        if (PackageManager.isEnabled(processor.session)) {
+            log.warn "The 'pixi' directive is deprecated when preview.package is enabled. Use 'package \"${config.pixi}\", provider: \"pixi\"' instead"
+        }
+
         final cache = new PixiCache(processor.session.getPixiConfig())
         cache.getCachePathFor(config.pixi as String)
     }
@@ -690,6 +702,36 @@ class TaskRun implements Cloneable {
         cache.getCachePathFor(config.spack as String, arch)
     }
 
+    PackageSpec getPackageSpec() {
+        // note: use an explicit function instead of a closure or lambda syntax
+        cache0.computeIfAbsent('packageSpec', new Function<String,PackageSpec>() {
+            @Override
+            PackageSpec apply(String it) {
+                return getPackageSpec0()
+            }})
+    }
+
+    private PackageSpec getPackageSpec0() {
+        if (!PackageManager.isEnabled(processor.session))
+            return null
+
+        if (!config.package)
+            return null
+
+        def packageManager = new PackageManager(processor.session)
+        
+        // Parse the package configuration
+        def packageDef = config.package
+        def defaultProvider = processor.session.config.navigate('packages.provider', 'conda') as String
+        
+        try {
+            return PackageManager.parseSpec(packageDef, defaultProvider)
+        } catch (Exception e) {
+            log.warn "Failed to parse package specification: ${e.message}"
+            return null
+        }
+    }
+
     protected ContainerInfo containerInfo() {
         // note: use an explicit function instead of a closure or lambda syntax, otherwise
         // when calling this method from a subclass it will result into a MissingMethodException

modules/nextflow/src/main/groovy/nextflow/script/ProcessConfig.groovy

@@ -89,6 +89,7 @@ class ProcessConfig implements Map<String,Object>, Cloneable {
             'maxRetries',
             'memory',
             'module',
+            'package',
             'penv',
             'pixi',
             'pod',