Fix module binaries PATH not injected on nextflow module run (#7087)

When a module is launched directly via `nextflow module run`, the module
main.nf is loaded as the entry script, so `ScriptMeta.isModule()` is
false and `TaskProcessor.getModuleBundle()` was returning null, causing
the `resources/usr/bin` directory not to be added to the task PATH.

Switch the gate from `isModule()` to `getScriptPath()` so the bundle is
resolved whenever the owner script has a known path. This makes the
behavior of `nextflow module run` consistent with `nextflow run` plus
include. The feature remains opt-in via `nextflow.enable.moduleBinaries`.

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>

Author: pditommaso

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

@@ -1569,7 +1569,11 @@ class TaskProcessor {
     ResourcesBundle getModuleBundle() {
         final script = this.getOwnerScript()
         final meta = ScriptMeta.get(script)
-        return meta?.isModule() ? meta.getModuleBundle() : null
+        // Resolve the resources bundle whenever the owner script has a known path,
+        // not only when it was loaded as an included module. This allows module
+        // binaries to be picked up also when a module is launched directly as the
+        // entry script via `nextflow module run` -- see #7087
+        return meta?.getScriptPath() ? meta.getModuleBundle() : null
     }
 
     @Memoized

modules/nextflow/src/test/groovy/nextflow/processor/TaskProcessorTest.groovy

@@ -35,6 +35,7 @@ import nextflow.script.BaseScript
 import nextflow.script.BodyDef
 import nextflow.script.ProcessConfig
 import nextflow.script.ProcessConfigV1
+import nextflow.script.ScriptMeta
 import nextflow.script.ScriptType
 import nextflow.script.bundle.ResourcesBundle
 import nextflow.script.params.FileInParam
@@ -100,6 +101,41 @@ class TaskProcessorTest extends Specification {
 
     }
 
+    def 'should resolve module bundle when script path is set regardless of isModule' () {
+        given:
+        def folder = Files.createTempDirectory('test')
+        def mod = folder.resolve('mod1'); mod.mkdir()
+        def bin = mod.resolve('resources/usr/bin'); bin.mkdirs()
+        def scriptPath = mod.resolve('main.nf'); Files.createFile(scriptPath)
+        Files.createFile(bin.resolve('echo.sh'))
+        and:
+        def script = Mock(BaseScript)
+        def meta = Mock(ScriptMeta) {
+            getScriptPath() >> scriptPath
+            // Simulate the failing case: script is loaded as the entry, not as an included module
+            isModule() >> false
+            getModuleBundle() >> ResourcesBundle.scan(mod.resolve('resources'))
+        }
+        and:
+        def session = Mock(Session) { getConfig() >> [:] }
+        def executor = Mock(Executor) {}
+        def processor = Spy(TaskProcessor, constructorArgs: [[session:session, executor:executor]])
+        processor.getOwnerScript() >> script
+
+        when:
+        ResourcesBundle bundle
+        GroovyMock(ScriptMeta, global: true)
+        ScriptMeta.get(script) >> meta
+        bundle = processor.getModuleBundle()
+
+        then:
+        bundle != null
+        bundle.getBinDirs() == [bin]
+
+        cleanup:
+        folder?.deleteDir()
+    }
+
     @Unroll
     def 'should add module bin paths to task env' () {
         given: