modify module list to skip subdirectories of directories that already contains the .module-info. This folders can't be a module

Signed-off-by: jorgee <jorge.ejarque@seqera.io>

Author: jorgee

modules/nextflow/src/main/groovy/nextflow/module/ModuleStorage.groovy

@@ -27,8 +27,11 @@ import org.apache.commons.compress.archivers.tar.TarArchiveOutputStream
 import org.apache.commons.compress.compressors.gzip.GzipCompressorInputStream
 import org.apache.commons.compress.compressors.gzip.GzipCompressorOutputStream
 
+import java.nio.file.FileVisitResult
 import java.nio.file.Files
 import java.nio.file.Path
+import java.nio.file.SimpleFileVisitor
+import java.nio.file.attribute.BasicFileAttributes
 import java.util.stream.Stream
 import java.util.zip.ZipEntry
 import java.util.zip.ZipInputStream
@@ -136,22 +139,28 @@ class ModuleStorage {
 
         List<InstalledModule> modules = []
 
-        try( final walkStream = Files.walk(modulesDir) ) {
-            walkStream
-                .filter { Path path -> Files.isDirectory(path) }
-                .filter { Path path -> Files.exists(path.resolve(MODULE_INFO_FILE)) }
-                .each { Path moduleDir ->
-                    try {
-                        def rel = modulesDir.relativize(moduleDir)
-                        if( rel.nameCount < 2 ) return  // Need at least scope/name
-                        def reference = ModuleReference.parse(rel.toString())
-                        def installed = getInstalledModule(reference)
-                        if( installed ) modules.add(installed)
-                    } catch(Exception e){
-                        // Catching exception to go on inspecting other valid folders
-                        log.debug("Not a valid module reference - $e.message")
+        try {
+            Files.walkFileTree(modulesDir, new SimpleFileVisitor<Path>() {
+                @Override
+                FileVisitResult preVisitDirectory(Path dir, BasicFileAttributes attrs) {
+                    if( dir == modulesDir ) return FileVisitResult.CONTINUE
+                    if( Files.exists(dir.resolve(MODULE_INFO_FILE)) ) {
+                        try {
+                            def rel = modulesDir.relativize(dir)
+                            if( rel.nameCount >= 2 ) {
+                                def reference = ModuleReference.parse(rel.toString())
+                                def installed = getInstalledModule(reference)
+                                if( installed ) modules.add(installed)
+                            }
+                        } catch(Exception e) {
+                            // Catching exception to go on inspecting other valid folders
+                            log.debug("Not a valid module reference - $e.message")
+                        }
+                        return FileVisitResult.SKIP_SUBTREE
                     }
+                    return FileVisitResult.CONTINUE
                 }
+            })
         } catch (IOException e) {
             log.warn "Failed to scan modules directory ${modulesDir}: ${e.message}"
         }

modules/nextflow/src/test/groovy/nextflow/module/ModuleStorageTest.groovy

@@ -207,6 +207,37 @@ class ModuleStorageTest extends Specification {
         ]
     }
 
+    def 'should ignore directories without MODULE_INFO_FILE and not descend into module subdirectories'() {
+        given:
+        def storage = new ModuleStorage(tempDir)
+
+        // A valid module with subdirectories (bin/, src/)
+        def moduleDir = storage.getModuleDir(new ModuleReference('nf-core', 'fastqc'))
+        Files.createDirectories(moduleDir)
+        moduleDir.resolve('main.nf').text = 'process FASTQC { }'
+        moduleDir.resolve('meta.yml').text = 'name: nf-core/fastqc\nversion: 1.0.0\n'
+        ModuleChecksum.save(moduleDir, 'checksum')
+        // Subdirectories inside the module — must NOT be listed as separate modules
+        def binDir = moduleDir.resolve('bin')
+        Files.createDirectories(binDir)
+        binDir.resolve('fastqc.sh').text = '#!/bin/bash'
+        def srcDir = moduleDir.resolve('src/main')
+        Files.createDirectories(srcDir)
+        srcDir.resolve('helper.groovy').text = 'def foo() {}'
+
+        // A plain directory tree with no MODULE_INFO_FILE anywhere — must be ignored entirely
+        def orphanDir = tempDir.resolve('modules/other-org/tool/deep/nested')
+        Files.createDirectories(orphanDir)
+        orphanDir.resolve('somefile.txt').text = 'not a module'
+
+        when:
+        def installed = storage.listInstalled()
+
+        then:
+        installed.size() == 1
+        installed[0].reference.fullName == 'nf-core/fastqc'
+    }
+
     def 'should return empty list when no modules installed'() {
         given:
         def storage = new ModuleStorage(tempDir)