Fix: nextflow inspect not resolving config-based container overrides

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

@@ -94,12 +94,6 @@ class ProcessDef extends BindableDef implements IterableDef, ChainableDef {
         str.split(Const.SCOPE_SEP).last()
     }
 
-    protected void initialize() {
-        // apply config settings to the process
-        final configProcessScope = (Map)session.config.process
-        new ProcessConfigBuilder(processConfig).applyConfig(configProcessScope, baseName, simpleName, processName)
-    }
-
     @Override
     ProcessDef clone() {
         def result = (ProcessDef)super.clone()
@@ -144,9 +138,6 @@ class ProcessDef extends BindableDef implements IterableDef, ChainableDef {
 
     @Override
     Object run(Object[] args) {
-        // initialise process config
-        initialize()
-
         // invoke process with legacy inputs/outputs
         if( processConfig instanceof ProcessConfigV1 )
             output = runV1(args, processConfig)
@@ -261,14 +252,23 @@ class ProcessDef extends BindableDef implements IterableDef, ChainableDef {
     }
 
     TaskProcessor createTaskProcessor() {
-        if( !processConfig )
-            initialize()
+        // apply process directives from config settings
+        applyConfig()
+
+        // create executor for process
         final executor = session
             .executorFactory
             .getExecutor(processName, processConfig, taskBody, session)
+
+        // create task processor for process
         return session
             .newProcessFactory(owner)
             .newTaskProcessor(processName, executor, processConfig, taskBody)
     }
 
+    protected void applyConfig() {
+        final configProcessScope = (Map)session.config.process
+        new ProcessConfigBuilder(processConfig).applyConfig(configProcessScope, baseName, simpleName, processName)
+    }
+
 }

modules/nextflow/src/test/groovy/nextflow/script/ProcessDefTest.groovy

@@ -1,6 +1,9 @@
 package nextflow.script
 
 import nextflow.Session
+import nextflow.executor.Executor
+import nextflow.executor.ExecutorFactory
+import nextflow.processor.TaskProcessor
 import spock.lang.Specification
 /**
  *
@@ -58,15 +61,15 @@ class ProcessDefTest extends Specification {
 
         when:
         def copy = proc.clone()
-        copy.initialize()
+        copy.applyConfig()
         then:
         def cfg1 = copy.processConfig.createTaskConfig()
         cfg1.getCpus()==2           // taken from the generic config
         cfg1.getMemory().giga == 3  // taken from the `foo` config
 
         when:
         copy = proc.cloneWithName('flow1:bar')
-        copy.initialize()
+        copy.applyConfig()
         then:
         def cfg2 = copy.processConfig.createTaskConfig()
         cfg2.getCpus()==4           // taken from the `bar` config
@@ -75,10 +78,38 @@ class ProcessDefTest extends Specification {
 
         when:
         copy = proc.cloneWithName('flow1:flow2:flow3:bar')
-        copy.initialize()
+        copy.applyConfig()
         then:
         def cfg3 = copy.processConfig.createTaskConfig()
         cfg3.getCpus()==4           // <-- taken from `withName: foo`
         cfg3.getMemory().giga == 8  // <-- taken from `withName: 'flow1:flow2:flow3:bar'`
     }
+
+    def 'should apply config when creating task processor' () {
+        given:
+        def OWNER = Mock(BaseScript)
+        def CONFIG = new ProcessConfig(OWNER, 'foo')
+        CONFIG.container = 'source-container:1.0'
+        def BODY = new BodyDef({->}, 'echo hello')
+        def proc = new ProcessDef(OWNER, 'foo', CONFIG, BODY)
+        and:
+        proc.session = Mock(Session) {
+            config >> [
+                process: [
+                    'withName:foo': [container: 'config-container:2.0']
+                ]
+            ]
+            executorFactory >> Mock(ExecutorFactory) {
+                getExecutor(_, _, _, _) >> Mock(Executor)
+            }
+            newProcessFactory(_) >> Mock(ProcessFactory) {
+                newTaskProcessor(_, _, _, _) >> Mock(TaskProcessor)
+            }
+        }
+
+        when:
+        proc.createTaskProcessor()
+        then:
+        proc.processConfig.container == 'config-container:2.0'
+    }
 }

modules/nextflow/src/test/groovy/nextflow/script/params/ParamsDsl2Test.groovy

@@ -34,7 +34,6 @@ class ParamsDsl2Test extends Dsl2Spec {
         def script = loadScript(SCRIPT)
         and:
         def process = ScriptMeta.get(script).getProcess('alpha')
-        process.initialize()
 
         then:
         def inputs = process.processConfig.getInputs()
@@ -70,7 +69,6 @@ class ParamsDsl2Test extends Dsl2Spec {
         def script = loadScript(SCRIPT)
         and:
         def process = ScriptMeta.get(script).getProcess('beta')
-        process.initialize()
 
         then:
         def inputs = process.processConfig.getInputs()