diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/module/CmdModuleInfo.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/module/CmdModuleInfo.groovy
index 56bc69708e..26a438a682 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/module/CmdModuleInfo.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/module/CmdModuleInfo.groovy
@@ -90,8 +90,7 @@ class CmdModuleInfo extends CmdBase {
             throw new AbortOperationException("Incorrect number of arguments")
         }
 
-        def moduleRef = '@' + args[0]
-        def reference = ModuleReference.parse(moduleRef)
+        def reference = ModuleReference.parse(args[0])
 
         // Get config
         def baseDir = root ?: Paths.get('.').toAbsolutePath().normalize()
@@ -117,10 +116,10 @@ class CmdModuleInfo extends CmdBase {
             log.warn "Failed to fetch metadata from registry: ${e.message}"
         }
         if( !release ) {
-            throw new AbortOperationException("No release information available for ${reference.nameWithoutPrefix}")
+            throw new AbortOperationException("No release information available for ${reference}")
         }
         if( !release.metadata ) {
-            log.info("No metadata found for $reference.nameWithoutPrefix ${release.version ? "($release.version)" : ''}")
+            log.info("No metadata found for $reference ${release.version ? "($release.version)" : ''}")
         }
         def moduleUrl = buildModuleUrl(registryConfig.url, reference, release.version)
         if( !output || output == 'text' ) {
@@ -135,7 +134,7 @@ class CmdModuleInfo extends CmdBase {
     private void printFormattedInfo(ModuleReference reference, ModuleRelease release, String moduleUrl) {
         ModuleMetadata metadata = release.metadata
         println ""
-        println "Module:      ${reference.nameWithoutPrefix}"
+        println "Module:      ${reference}"
         println "Version:     ${release.version}"
         println "URL:         ${moduleUrl}"
         println "Description: ${metadata.description ?: release.description ?: 'N/A'}"
@@ -218,7 +217,7 @@ class CmdModuleInfo extends CmdBase {
 
     private List<String> generateUsageTemplate(ModuleReference reference, ModuleMetadata metadata) {
         def template = new ArrayList<String>()
-        template.add("nextflow module run ${reference.nameWithoutPrefix}".toString())
+        template.add("nextflow module run ${reference}".toString())
         if( version )
             template.add(" -version $version".toString())
 
@@ -281,7 +280,7 @@ class CmdModuleInfo extends CmdBase {
     private void printJsonInfo(ModuleReference reference, ModuleRelease release, String moduleUrl) {
         def metadata = release?.metadata
         def info = [
-            name       : reference.nameWithoutPrefix,
+            name       : reference.toString(),
             fullName   : reference.fullName,
             version    : release.version,
             url        : moduleUrl,
diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/module/CmdModuleInstall.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/module/CmdModuleInstall.groovy
index f509aef73e..bcc52b6ed7 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/module/CmdModuleInstall.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/module/CmdModuleInstall.groovy
@@ -70,9 +70,7 @@ class CmdModuleInstall extends CmdBase {
             throw new AbortOperationException("Incorrect number of arguments")
         }
 
-        def moduleRef = '@' + args[0]
-
-        def reference = ModuleReference.parse(moduleRef)
+        def reference = ModuleReference.parse(args[0])
 
         // Get config
         def baseDir = root ?: Paths.get('.').toAbsolutePath().normalize()
@@ -96,7 +94,7 @@ class CmdModuleInstall extends CmdBase {
             def installedVersion = version ?: resolver.resolveVersion(reference)
             specFile.addModuleEntry(reference.fullName, installedVersion)
 
-            println "Module ${reference.nameWithoutPrefix}@${installedVersion} installed and configured successfully"
+            println "Module ${reference}@${installedVersion} installed and configured successfully"
         }
         catch( AbortOperationException e ) {
             throw e
diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/module/CmdModuleList.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/module/CmdModuleList.groovy
index b4919b0c68..5992196c2b 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/module/CmdModuleList.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/module/CmdModuleList.groovy
@@ -111,7 +111,7 @@ class CmdModuleList extends CmdBase {
 
         installed.each { module ->
             def status = getStatusString(module.integrity)
-            println "${module.reference.nameWithoutPrefix.padRight(40)}${(module.installedVersion ?: 'unknown').padRight(15)}${status}"
+            println "${module.reference.toString().padRight(40)}${(module.installedVersion ?: 'unknown').padRight(15)}${status}"
         }
         println ""
     }
@@ -119,7 +119,7 @@ class CmdModuleList extends CmdBase {
     private void printJsonList(List<InstalledModule> installed) {
         def modules = installed.collect { module ->
             [
-                name     : module.reference.nameWithoutPrefix,
+                name     : module.reference.toString(),
                 version  : module.installedVersion ?: 'unknown',
                 integrity: module.integrity.toString(),
                 directory: module.directory.toString()
@@ -136,8 +136,8 @@ class CmdModuleList extends CmdBase {
                 return 'OK'
             case ModuleIntegrity.MODIFIED:
                 return 'MODIFIED'
-            case ModuleIntegrity.MISSING_CHECKSUM:
-                return 'NO CHECKSUM'
+            case ModuleIntegrity.NO_REMOTE_MODULE:
+                return 'LOCAL'
             case ModuleIntegrity.CORRUPTED:
                 return 'CORRUPTED'
             default:
diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/module/CmdModulePublish.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/module/CmdModulePublish.groovy
index a3b46056fc..23cc9f74cc 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/module/CmdModulePublish.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/module/CmdModulePublish.groovy
@@ -25,6 +25,7 @@ import nextflow.cli.CmdBase
 import nextflow.config.ConfigBuilder
 import nextflow.config.RegistryConfig
 import nextflow.exception.AbortOperationException
+import nextflow.module.ModuleChecksum
 import nextflow.module.ModuleSpec
 import nextflow.module.ModuleReference
 import nextflow.module.ModuleRegistryClient
@@ -60,6 +61,9 @@ class CmdModulePublish extends CmdBase {
     @TestOnly
     protected ModuleRegistryClient client
 
+    //Flag if publish is invoked from a scope/name. In this case we should create/update the .module-info with the correct checksum
+    private boolean useModuleReference = false
+
     @Override
     String getName() {
         return 'publish'
@@ -115,14 +119,10 @@ class CmdModulePublish extends CmdBase {
 
     private void publishModule(Path moduleDir, RegistryConfig registryConfig, ModuleSpec manifest){
         log.info "Creating module bundle..."
-        def storage = new ModuleStorage(moduleDir.parent)
         def tempBundleFile = Files.createTempFile("nf-module-publish-", ".tar.gz")
 
         try {
-            storage.createBundle(moduleDir, tempBundleFile)
-
-            // Compute bundle checksum
-            def checksum = storage.computeBundleChecksum(tempBundleFile)
+            def checksum = ModuleStorage.createBundle(moduleDir, tempBundleFile)
             log.info "Bundle checksum: ${checksum}"
 
             // Read bundle content as bytes
@@ -139,6 +139,14 @@ class CmdModulePublish extends CmdBase {
             def registryClient = new ModuleRegistryClient(registryConfig)
             def response = registryClient.publishModule(manifest.name, request, registryUrl)
 
+            if (useModuleReference) {
+                // If publish is performed using the module reference we should create/update the .module-info with the correct checksum
+                try {
+                    ModuleChecksum.save(moduleDir, ModuleChecksum.compute(moduleDir))
+                }catch (Exception e){
+                    log.warn("Unable to save the checksum - ${e.message}")
+                }
+            }
             println "✓ Module published successfully!"
             println ""
             println "Module details:"
@@ -246,13 +254,13 @@ class CmdModulePublish extends CmdBase {
             return Paths.get(module).toAbsolutePath().normalize()
         }
 
-        final ref =  ModuleReference.parse('@' + module)
+        final ref =  ModuleReference.parse(module)
         final localStorage = new ModuleStorage(root ?: Paths.get('.').toAbsolutePath().normalize())
 
         if (!localStorage.isInstalled(ref)){
             throw new AbortOperationException("No module diretory found for $module")
         }
-
+        useModuleReference = true
         return localStorage.getModuleDir(ref)
     }
 }
diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/module/CmdModuleRemove.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/module/CmdModuleRemove.groovy
index b793974f32..3c3ab9d026 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/module/CmdModuleRemove.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/module/CmdModuleRemove.groovy
@@ -68,9 +68,7 @@ class CmdModuleRemove extends CmdBase {
             throw new AbortOperationException("Cannot use both -keep-config and -keep-files flags together")
         }
 
-        def moduleRef = '@' + args[0]
-
-        def reference = ModuleReference.parse(moduleRef)
+        def reference = ModuleReference.parse(args[0])
 
         // Get config
         def baseDir = root ?: Paths.get('.').toAbsolutePath().normalize()
@@ -87,15 +85,15 @@ class CmdModuleRemove extends CmdBase {
 
             // Remove local files unless -keep-files is set
             if( !keepFiles ) {
-                println "Removing module files for ${reference.nameWithoutPrefix}..."
+                println "Removing module files for ${reference}..."
                 filesRemoved = storage.removeModule(reference)
                 if( filesRemoved ) {
                     println "Module files removed successfully"
                 } else {
-                    println "Module ${reference.nameWithoutPrefix} was not installed locally"
+                    println "Module ${reference} was not installed locally"
                 }
             } else {
-                println "Keeping module files for ${reference.nameWithoutPrefix} (due to -keep-files flag)"
+                println "Keeping module files for ${reference} (due to -keep-files flag)"
             }
 
             // Remove config entry unless -keep-config is set
@@ -105,7 +103,7 @@ class CmdModuleRemove extends CmdBase {
                 if( configRemoved ) {
                     println "Module entry removed from configuration"
                 } else {
-                    println "Module ${reference.nameWithoutPrefix} was not configured in nextflow_spec.json"
+                    println "Module ${reference} was not configured in nextflow_spec.json"
                 }
             } else {
                 println "Keeping module entry in nextflow_spec.json (due to -keep-config flag)"
@@ -113,9 +111,9 @@ class CmdModuleRemove extends CmdBase {
 
             // Summary
             if( filesRemoved || configRemoved ) {
-                println "\nModule ${reference.nameWithoutPrefix} removal completed"
+                println "\nModule ${reference} removal completed"
             } else {
-                println "\nModule ${reference.nameWithoutPrefix} was not found"
+                println "\nModule ${reference} was not found"
             }
         }
         catch( AbortOperationException e ) {
diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/module/CmdModuleRun.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/module/CmdModuleRun.groovy
index 4212ae0d2d..56f3cf18bf 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/module/CmdModuleRun.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/module/CmdModuleRun.groovy
@@ -61,15 +61,12 @@ class CmdModuleRun extends CmdRun {
             throw new AbortOperationException("Arguments not provided")
         }
 
-        // Parse module reference (first argument starting with @)
-        String moduleRef = '@' + args[0]
-
         // Parse and validate module reference
         ModuleReference reference
         try {
-            reference = ModuleReference.parse(moduleRef)
+            reference = ModuleReference.parse(args[0])
         } catch( Exception e ) {
-            throw new AbortOperationException("Invalid module reference: ${moduleRef}", e)
+            throw new AbortOperationException("Invalid module reference: ${args[0]}", e)
         }
 
         // Get config
diff --git a/modules/nextflow/src/main/groovy/nextflow/module/DefaultRemoteModuleResolver.groovy b/modules/nextflow/src/main/groovy/nextflow/module/DefaultRemoteModuleResolver.groovy
index ac94aef557..e1db3366f0 100644
--- a/modules/nextflow/src/main/groovy/nextflow/module/DefaultRemoteModuleResolver.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/module/DefaultRemoteModuleResolver.groovy
@@ -67,7 +67,7 @@ class DefaultRemoteModuleResolver implements RemoteModuleResolver {
             // Resolve module (will auto-install if missing or version mismatch)
             def mainFile = resolver.resolve(reference, null, true)
 
-            log.info "Module ${reference.nameWithoutPrefix} resolved to ${mainFile}"
+            log.debug "Module ${reference} resolved to ${mainFile}"
             return mainFile
         } catch (Exception e) {
             throw new IllegalModulePath(
@@ -97,4 +97,4 @@ class DefaultRemoteModuleResolver implements RemoteModuleResolver {
         }
         return new ModulesConfig(modules)
     }
-}
\ No newline at end of file
+}
diff --git a/modules/nextflow/src/main/groovy/nextflow/module/InstalledModule.groovy b/modules/nextflow/src/main/groovy/nextflow/module/InstalledModule.groovy
index cb032d6c2a..88fddb02a6 100644
--- a/modules/nextflow/src/main/groovy/nextflow/module/InstalledModule.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/module/InstalledModule.groovy
@@ -39,7 +39,7 @@ class InstalledModule {
     Path directory
     Path mainFile
     Path manifestFile
-    Path checksumFile
+    Path moduleInfoFile
     String installedVersion
     String expectedChecksum
 
@@ -54,9 +54,9 @@ class InstalledModule {
             return ModuleIntegrity.CORRUPTED
         }
 
-        // Check if checksum file exists
-        if( !Files.exists(checksumFile) ) {
-            return ModuleIntegrity.MISSING_CHECKSUM
+        // Check if .module-info file exists
+        if( !Files.exists(moduleInfoFile) ) {
+            return ModuleIntegrity.NO_REMOTE_MODULE
         }
 
         try {
@@ -71,7 +71,7 @@ class InstalledModule {
                 return ModuleIntegrity.MODIFIED
             }
         } catch( Exception e ) {
-            log.warn "Failed to compute checksum for module ${reference.nameWithoutPrefix}: ${e.message}"
+            log.warn "Failed to compute checksum for module ${reference}: ${e.message}"
             return ModuleIntegrity.CORRUPTED
         }
     }
@@ -84,6 +84,6 @@ class InstalledModule {
 enum ModuleIntegrity {
     VALID,              // Checksum matches
     MODIFIED,           // Checksum mismatch (local changes)
-    MISSING_CHECKSUM,   // No .checksum file
+    NO_REMOTE_MODULE,   // No .module-info file (local-only module, no registry origin)
     CORRUPTED           // Missing required files
 }
diff --git a/modules/nextflow/src/main/groovy/nextflow/module/ModuleChecksum.groovy b/modules/nextflow/src/main/groovy/nextflow/module/ModuleChecksum.groovy
index fc795f1b60..94235bc696 100644
--- a/modules/nextflow/src/main/groovy/nextflow/module/ModuleChecksum.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/module/ModuleChecksum.groovy
@@ -33,7 +33,7 @@ import java.security.MessageDigest
 class ModuleChecksum {
 
     public static final String CHECKSUM_ALGORITHM = "SHA-256"
-    public static final String CHECKSUM_FILE = ".checksum"
+    public static final String MODULE_INFO_FILE = ".module-info"
 
     /**
      * Compute the SHA-256 checksum of a module directory
@@ -54,7 +54,7 @@ class ModuleChecksum {
             try( final walkStream = Files.walk(moduleDir) ) {
                 walkStream
                     .filter { Path path -> Files.isRegularFile(path) }
-                    .filter { Path path -> !path.fileName.toString().equals(CHECKSUM_FILE) }
+                    .filter { Path path -> !path.fileName.toString().equals(MODULE_INFO_FILE) }
                     .sorted()
                     .each { Path path -> files.add(path) }
             }
@@ -85,28 +85,35 @@ class ModuleChecksum {
     }
 
     /**
-     * Save a checksum to the .checksum file in the module directory
+     * Save a checksum to the .module-info file in the module directory
      *
      * @param moduleDir The module directory path
      * @param checksum The checksum to save
      */
     static void save(Path moduleDir, String checksum) {
-        def checksumFile = moduleDir.resolve(CHECKSUM_FILE)
-        Files.writeString(checksumFile, checksum)
+        def moduleInfoFile = moduleDir.resolve(MODULE_INFO_FILE)
+        def props = new Properties()
+        // If file exists loads to update current just checksum property
+        if( Files.exists( moduleInfoFile))
+            moduleInfoFile.withInputStream { is -> props.load(is) }
+        props.setProperty('checksum', checksum)
+        moduleInfoFile.withOutputStream { os -> props.store(os, null) }
     }
 
     /**
-     * Load a checksum from the .checksum file in the module directory
+     * Load a checksum from the .module-info file in the module directory
      *
      * @param moduleDir The module directory path
      * @return The checksum, or null if file doesn't exist
      */
     static String load(Path moduleDir) {
-        def checksumFile = moduleDir.resolve(CHECKSUM_FILE)
-        if( !Files.exists(checksumFile) ) {
+        def moduleInfoFile = moduleDir.resolve(MODULE_INFO_FILE)
+        if( !Files.exists(moduleInfoFile) ) {
             return null
         }
-        return checksumFile.text
+        def props = new Properties()
+        moduleInfoFile.withInputStream { is -> props.load(is) }
+        return props.getProperty('checksum')
     }
 
     /**
diff --git a/modules/nextflow/src/main/groovy/nextflow/module/ModuleReference.groovy b/modules/nextflow/src/main/groovy/nextflow/module/ModuleReference.groovy
index 12bff1c6ac..23cbf7ba3d 100644
--- a/modules/nextflow/src/main/groovy/nextflow/module/ModuleReference.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/module/ModuleReference.groovy
@@ -34,7 +34,7 @@ class ModuleReference {
     // Pattern allows: optional @, scope with letters/digits/hyphens/dots/underscores, name segments separated by slashes (no trailing slash)
     // Scope: starts with letter/digit, followed by letters/digits/dots/underscores/hyphens
     // Name: one or more segments (each starting with letter, followed by letters/digits/underscores/hyphens), separated by slashes
-    private static final Pattern MODULE_NAME_PATTERN = ~/^@?([a-z0-9][a-z0-9._\-]*)\/([a-z][a-z0-9_\-]*(?:\/[a-z][a-z0-9_\-]*)*)$/
+    private static final Pattern MODULE_NAME_PATTERN = ~/^([a-z0-9][a-z0-9._\-]*)\/([a-z][a-z0-9._\-]*(?:\/[a-z][a-z0-9._\-]*)*)$/
 
     final String scope
     final String name
@@ -43,7 +43,7 @@ class ModuleReference {
     ModuleReference(String scope, String name) {
         this.scope = scope
         this.name = name
-        this.fullName = "@${scope}/${name}"
+        this.fullName = "${scope}/${name}"
     }
 
     /**
@@ -65,7 +65,7 @@ class ModuleReference {
         if( !matcher.matches() ) {
             throw new AbortOperationException(
                 "Invalid module reference: '${source}'. " +
-                    "Expected format: [@]scope/name where scope is lowercase alphanumeric with dots/underscores/hyphens " +
+                    "Expected format: scope/name where scope is lowercase alphanumeric with dots/underscores/hyphens " +
                     "and name is lowercase alphanumeric with underscores/hyphens, optionally with slash-separated segments"
             )
         }
@@ -73,15 +73,6 @@ class ModuleReference {
         return new ModuleReference(matcher.group(1), matcher.group(2))
     }
 
-    /**
-     * Get the module name without the @ prefix
-     *
-     * @return Module name in format "scope/name"
-     */
-    String getNameWithoutPrefix() {
-        return "${scope}/${name}"
-    }
-
     @Override
     String toString() {
         return fullName
diff --git a/modules/nextflow/src/main/groovy/nextflow/module/ModuleRegistryClient.groovy b/modules/nextflow/src/main/groovy/nextflow/module/ModuleRegistryClient.groovy
index fa1d827622..4b2fc225ec 100644
--- a/modules/nextflow/src/main/groovy/nextflow/module/ModuleRegistryClient.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/module/ModuleRegistryClient.groovy
@@ -56,10 +56,7 @@ class ModuleRegistryClient {
     }
 
     private String encodeName(String name) {
-        return URLEncoder.encode(
-            name.startsWith('@') ? name.substring(1) : name,
-            'UTF-8'
-        )
+        return URLEncoder.encode(name, 'UTF-8')
     }
 
     /**
@@ -443,11 +440,7 @@ class ModuleRegistryClient {
                     "  }\n"
             )
         }
-        try {
-            return publishModuleToRegistry(registryUrl, name, request, authToken)
-        } catch( Exception e ) {
-            throw new AbortOperationException("Failed to publish to ${registryUrl}", e)
-        }
+        return publishModuleToRegistry(registryUrl, name, request, authToken)
     }
 
     /**
diff --git a/modules/nextflow/src/main/groovy/nextflow/module/ModuleResolver.groovy b/modules/nextflow/src/main/groovy/nextflow/module/ModuleResolver.groovy
index 11ad0f2335..a5a55c2fe8 100644
--- a/modules/nextflow/src/main/groovy/nextflow/module/ModuleResolver.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/module/ModuleResolver.groovy
@@ -69,25 +69,27 @@ class ModuleResolver {
             def integrity = installed.integrity
             if( integrity == ModuleIntegrity.CORRUPTED ) {
                 throw new AbortOperationException(
-                    "Module ${reference.nameWithoutPrefix} is corrupted (missing required files). " +
+                    "Module ${reference} is corrupted (missing required files). " +
                         "Please remove and reinstall."
                 )
             }
 
             if( integrity == ModuleIntegrity.MODIFIED ) {
-                log.warn "Module ${reference.nameWithoutPrefix} has local modifications (checksum mismatch)"
+                log.warn1 "Module ${reference} has local modifications (checksum mismatch)"
+            } else if( integrity == ModuleIntegrity.NO_REMOTE_MODULE ) {
+                log.warn1 "Module ${reference} has no registry origin (.module-info missing)"
             }
 
             // Check if version matches
             if( targetVersion && installed.installedVersion != targetVersion ) {
                 if( autoInstall ) {
-                    log.info "Upgrading module ${reference.nameWithoutPrefix} from ${installed.installedVersion} to ${targetVersion}"
+                    log.info "Upgrading module ${reference} from ${installed.installedVersion} to ${targetVersion}"
                     return installModule(reference, targetVersion)
                 } else {
                     throw new AbortOperationException(
-                        "Module ${reference.nameWithoutPrefix} version mismatch: " +
+                        "Module ${reference} version mismatch: " +
                             "installed=${installed.installedVersion}, required=${targetVersion}. " +
-                            "Run 'nextflow module install ${reference.nameWithoutPrefix}@${targetVersion}' to update."
+                            "Run 'nextflow module install ${reference}@${targetVersion}' to update."
                     )
                 }
             }
@@ -101,17 +103,17 @@ class ModuleResolver {
             return installModule(reference, targetVersion)
         } else {
             throw new AbortOperationException(
-                "Module ${reference.nameWithoutPrefix} is not installed. " +
-                    "Run 'nextflow module install ${reference.nameWithoutPrefix}' to install."
+                "Module ${reference} is not installed. " +
+                    "Run 'nextflow module install ${reference}' to install."
             )
         }
     }
 
     String resolveVersion(ModuleReference reference) {
         final version = modulesConfig.getVersion(reference.fullName)
-            ?: registryClient.fetchModule(reference.fullName).latest?.version
+            ?: registryClient.fetchModule(reference.fullName)?.latest?.version
         if( !version ) {
-            throw new AbortOperationException("Module ${reference.nameWithoutPrefix} has no published versions")
+            throw new AbortOperationException("Module ${reference} has no published versions")
         }
         return version
     }
@@ -131,7 +133,7 @@ class ModuleResolver {
         if( storage.isInstalled(reference) ) {
             def installed = storage.getInstalledModule(reference)
             if( installed.installedVersion == version ) {
-                log.info "Module ${reference.nameWithoutPrefix}@${installed.installedVersion} is already installed (version $version)"
+                log.info "Module ${reference}@${installed.installedVersion} is already installed (version $version)"
                 return installed.mainFile
             }
 
@@ -139,14 +141,20 @@ class ModuleResolver {
             def integrity = installed.integrity
             if( integrity == ModuleIntegrity.MODIFIED && !force ) {
                 throw new AbortOperationException(
-                    "Module ${reference.nameWithoutPrefix} has local modifications. " +
+                    "Module ${reference} has local modifications. " +
+                        "Use --force to override, or save your changes first."
+                )
+            }
+            if( integrity == ModuleIntegrity.NO_REMOTE_MODULE && !force ) {
+                throw new AbortOperationException(
+                    " Folder 'modules/${reference}' already exists and is not a valid remote module. " +
                         "Use --force to override, or save your changes first."
                 )
             }
         }
 
 
-        log.info "Installing module ${reference.nameWithoutPrefix}@${version}..."
+        log.info "Installing module ${reference}@${version}..."
 
         // Download module package to temporary location
         Path tempFile = Files.createTempFile("nf-module-", ".tgz")
@@ -157,7 +165,7 @@ class ModuleResolver {
             // Install to modules directory (will compute directory checksum for future integrity checks)
             InstalledModule installed = storage.installModule(reference, version, tempFile)
 
-            log.info "Module ${reference.nameWithoutPrefix}@${version} installed successfully at ${installed.mainFile.parent}"
+            log.info "Module ${reference}@${version} installed successfully at ${installed.mainFile.parent}"
             return installed.mainFile
         }
         finally {
diff --git a/modules/nextflow/src/main/groovy/nextflow/module/ModuleStorage.groovy b/modules/nextflow/src/main/groovy/nextflow/module/ModuleStorage.groovy
index 97802c711d..9cffaa0279 100644
--- a/modules/nextflow/src/main/groovy/nextflow/module/ModuleStorage.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/module/ModuleStorage.groovy
@@ -70,7 +70,7 @@ class ModuleStorage {
      * @return The module directory path
      */
     Path getModuleDir(ModuleReference reference) {
-        return modulesDir.resolve("@${reference.scope}").resolve(reference.name)
+        return modulesDir.resolve(reference.scope).resolve(reference.name)
     }
 
     /**
@@ -101,7 +101,7 @@ class ModuleStorage {
             directory: moduleDir,
             mainFile: moduleDir.resolve(Const.DEFAULT_MAIN_FILE_NAME),
             manifestFile: moduleDir.resolve(MODULE_MANIFEST_FILE),
-            checksumFile: moduleDir.resolve(ModuleChecksum.CHECKSUM_FILE),
+            moduleInfoFile: moduleDir.resolve(ModuleChecksum.MODULE_INFO_FILE),
         )
 
         // Load checksum if available
@@ -111,7 +111,7 @@ class ModuleStorage {
     }
 
     /**
-     * List all installed modules
+     * List all installed modules by scanning for directories containing a .module-info marker file.
      *
      * @return List of InstalledModule objects
      */
@@ -122,63 +122,27 @@ class ModuleStorage {
 
         List<InstalledModule> modules = []
 
-        // Iterate over scope directories
-        try( final scopeStream = Files.list(modulesDir) ){
-            scopeStream.each { Path scopeDir ->
-                if (!Files.isDirectory(scopeDir)) return
-
-                def scopeDirName = scopeDir.fileName.toString()
-                // Remove @ prefix from directory name to get scope
-                def scope = scopeDirName.startsWith('@') ? scopeDirName.substring(1) : scopeDirName
-
-                // Recursively find all directories containing meta.yml under this scope
-                findModulesRecursive(scopeDir, scope, modules)
-            }
-        }
-
-        return modules
-    }
-
-    /**
-     * Recursively find modules in subdirectories
-     * @param dir Current directory to search
-     * @param scope Module scope
-     * @param modules List to accumulate found modules
-     */
-    private void findModulesRecursive(Path dir, String scope, List<InstalledModule> modules) {
-        if (!Files.isDirectory(dir)) return
-
-        // Check if current directory contains meta.yml (is a module)
-        if (Files.exists(dir.resolve(MODULE_MANIFEST_FILE))) {
-            // Calculate the module name from the path relative to scope directory
-            def scopeDir = dir.getParent()
-            while (scopeDir != null && !scopeDir.fileName.toString().equals('@' + scope)) {
-                scopeDir = scopeDir.getParent()
-            }
-
-            if (scopeDir != null) {
-                def relativePath = scopeDir.relativize(dir).toString()
-                def name = relativePath.replace('\\', '/') // Normalize path separators
-                def reference = new ModuleReference(scope, name)
-
-                def installed = getInstalledModule(reference)
-                if (installed) {
-                    modules.add(installed)
-                }
-            }
-        }
-
-        // Recursively search subdirectories
-        try (final subStream = Files.list(dir) ) {
-                subStream.each { Path subDir ->
-                    if (Files.isDirectory(subDir)) {
-                        findModulesRecursive(subDir, scope, modules)
+        try( final walkStream = Files.walk(modulesDir) ) {
+            walkStream
+                .filter { Path path -> Files.isDirectory(path) }
+                .filter { Path path -> Files.exists(path.resolve(ModuleChecksum.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")
                     }
                 }
-
         } catch (IOException e) {
-            log.warn "Failed to list directory ${dir}: ${e.message}"
+            log.warn "Failed to scan modules directory ${modulesDir}: ${e.message}"
         }
+
+        return modules
     }
 
     /**
@@ -214,7 +178,7 @@ class ModuleStorage {
             def checksum = ModuleChecksum.compute(moduleDir)
             ModuleChecksum.save(moduleDir, checksum)
 
-            log.debug "Installed module ${reference.nameWithoutPrefix}@${version} to ${moduleDir}"
+            log.debug "Installed module ${reference}@${version} to ${moduleDir}"
 
             return getInstalledModule(reference)
         }
@@ -227,7 +191,7 @@ class ModuleStorage {
                     log.warn "Failed to clean up after installation failure: ${cleanupError.message}"
                 }
             }
-            throw new AbortOperationException("Failed to install module ${reference.nameWithoutPrefix}@${version}", e)
+            throw new AbortOperationException("Failed to install module ${reference}@${version}", e)
         }
     }
 
@@ -246,7 +210,7 @@ class ModuleStorage {
 
         try {
             FileHelper.deletePath(moduleDir)
-            log.debug "Removed module: ${reference.nameWithoutPrefix}"
+            log.debug "Removed module: ${reference}"
 
             // Clean up empty scope directory
             def scopeDir = moduleDir.parent
@@ -257,7 +221,7 @@ class ModuleStorage {
             return true
         }
         catch (Exception e) {
-            throw new AbortOperationException("Failed to remove module ${reference.nameWithoutPrefix}", e)
+            throw new AbortOperationException("Failed to remove module ${reference}", e)
         }
     }
 
@@ -362,9 +326,9 @@ class ModuleStorage {
      *
      * @param moduleDir The module directory to bundle
      * @param targetFile The target bundle file path
-     * @return The created bundle file with its checksum
+     * @return The created bundle file checksum
      */
-    Path createBundle(Path moduleDir, Path targetFile) {
+    static String createBundle(Path moduleDir, Path targetFile) {
         if (!Files.exists(moduleDir) || !Files.isDirectory(moduleDir)) {
             throw new AbortOperationException("Module directory not found: ${moduleDir}")
         }
@@ -384,9 +348,9 @@ class ModuleStorage {
                     }
                 }
             }
-
-            log.debug "Created module bundle: ${targetFile} (size: ${Files.size(targetFile)} bytes)"
-            return targetFile
+            final checksum = computeBundleChecksum(targetFile)
+            log.debug "Created module bundle: ${targetFile} (size: ${Files.size(targetFile)} bytes, checksum: $checksum)"
+            return checksum
         }
         catch (Exception e) {
             // Clean up partial file on failure
@@ -408,12 +372,12 @@ class ModuleStorage {
      * @param sourceDir The source directory being archived
      * @param currentPath The current path being added
      */
-    private void addToTarArchive(TarArchiveOutputStream tos, Path sourceDir, Path currentPath) {
+    private static void addToTarArchive(TarArchiveOutputStream tos, Path sourceDir, Path currentPath) {
 
         try ( def tarStream = Files.list(currentPath)) {
             tarStream.each { Path path ->
-                // Skip .checksum file when creating bundle
-                if (path.fileName.toString() == ModuleChecksum.CHECKSUM_FILE) {
+                // Skip .module-info file when creating bundle
+                if (path.fileName.toString() == ModuleChecksum.MODULE_INFO_FILE) {
                     return
                 }
 
@@ -447,7 +411,7 @@ class ModuleStorage {
      * @param bundleFile The bundle file
      * @return The SHA-256 checksum as hex string
      */
-    String computeBundleChecksum(Path bundleFile) {
+    static String computeBundleChecksum(Path bundleFile) {
         if (!Files.exists(bundleFile)) {
             throw new AbortOperationException("Bundle file not found: ${bundleFile}")
         }
diff --git a/modules/nextflow/src/main/groovy/nextflow/pipeline/PipelineSpec.groovy b/modules/nextflow/src/main/groovy/nextflow/pipeline/PipelineSpec.groovy
index 766b71f62e..2e109cdc4f 100644
--- a/modules/nextflow/src/main/groovy/nextflow/pipeline/PipelineSpec.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/pipeline/PipelineSpec.groovy
@@ -51,8 +51,8 @@ class PipelineSpec {
      * @param version The module version
      */
     void addModuleEntry(String moduleName, String version) {
-        // Normalize module name (ensure it starts with @)
-        def normalizedName = moduleName.startsWith('@') ? moduleName : '@' + moduleName
+        // Normalize module name (strip leading @ if present)
+        def normalizedName = moduleName.startsWith('@') ? moduleName.substring(1) : moduleName
 
         def spec = readSpecFile()
 
@@ -80,8 +80,6 @@ class PipelineSpec {
      * @return true if entry was removed, false if it didn't exist
      */
     boolean removeModuleEntry(String moduleName) {
-        // Normalize module name (ensure it starts with @)
-        def normalizedName = moduleName.startsWith('@') ? moduleName : '@' + moduleName
 
         def spec = readSpecFile()
 
@@ -89,10 +87,10 @@ class PipelineSpec {
              return false
         }
         final modules = spec.modules as Map<String,String>
-        if( modules.remove(normalizedName) == null )
+        if( modules.remove(moduleName) == null )
             return false
         writeSpecFile(spec)
-        log.info "Removed ${normalizedName} from ${SPEC_FILE_NAME}"
+        log.info "Removed ${moduleName} from ${SPEC_FILE_NAME}"
         return true
     }
     /**
@@ -145,4 +143,4 @@ class PipelineSpec {
             throw new RuntimeException("Failed to write spec file ${specFile}: ${e.message}", e)
         }
     }
-}
\ No newline at end of file
+}
diff --git a/modules/nextflow/src/main/groovy/nextflow/script/IncludeDef.groovy b/modules/nextflow/src/main/groovy/nextflow/script/IncludeDef.groovy
index 60a54044b5..531e6c4cc4 100644
--- a/modules/nextflow/src/main/groovy/nextflow/script/IncludeDef.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/script/IncludeDef.groovy
@@ -29,6 +29,7 @@ import nextflow.NF
 import nextflow.Session
 import nextflow.exception.IllegalModulePath
 import nextflow.exception.ScriptCompilationException
+import nextflow.module.ModuleReference
 import nextflow.module.spi.RemoteModuleResolverProvider
 import nextflow.plugin.Plugins
 import nextflow.plugin.extension.PluginExtensionProvider
@@ -163,16 +164,17 @@ class IncludeDef {
     @PackageScope
     Path resolveModulePath(include) {
         assert include
-        if( include.toString().startsWith('@') ) {
-            return resolveRemoteModulePath(include.toString())
-        }
         final result = include as Path
         if( result.isAbsolute() ) {
             if( result.scheme == 'file' ) return result
             throw new IllegalModulePath("Cannot resolve module path: ${result.toUriString()}")
         }
-
-        return getOwnerPath().resolveSibling(include.toString())
+        final str = include.toString()
+        if( str.startsWith('./') || str.startsWith('../') ) {
+            return getOwnerPath().resolveSibling(str).normalize()
+        }
+        // Not a local path — treat as remote module reference (scope/name)
+        return resolveRemoteModulePath(str)
     }
 
     @PackageScope
@@ -216,9 +218,15 @@ class IncludeDef {
             throw new IllegalModulePath("Remote modules are not allowed -- Offending module: ${path.toUriString()}")
 
         final str = path.toString()
-        if( !str.startsWith('/') && !str.startsWith('./') && !str.startsWith('../') && !str.startsWith('plugin/') && !str.startsWith('@') )
-            throw new IllegalModulePath("Module path must start with '/' , './' or '@' prefix -- Offending module: $str")
+        if( str.startsWith('/') || str.startsWith('./') || str.startsWith('../') || str.startsWith('plugin/') )
+            return
 
+        // Otherwise must be a valid remote module reference in scope/name format
+        try {
+            ModuleReference.parse(str)
+        } catch( Exception e ) {
+            throw new IllegalModulePath("Module path must start with '/', './', '../' or 'plugin/' prefix, or be a valid remote module reference (scope/name) -- Offending module: $str")
+        }
     }
 
     @PackageScope
diff --git a/modules/nextflow/src/test/groovy/nextflow/cli/module/CmdModuleInfoTest.groovy b/modules/nextflow/src/test/groovy/nextflow/cli/module/CmdModuleInfoTest.groovy
index 7668fa7cf7..ba90e5d005 100644
--- a/modules/nextflow/src/test/groovy/nextflow/cli/module/CmdModuleInfoTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/cli/module/CmdModuleInfoTest.groovy
@@ -177,7 +177,7 @@ class CmdModuleInfoTest extends Specification {
 
         then:
         json.name == 'nf-core/fastqc'
-        json.fullName == '@nf-core/fastqc'
+        json.fullName == 'nf-core/fastqc'
         json.version == '1.0.0'
         json.description == 'FastQC quality control'
         json.authors == ['nf-core']
diff --git a/modules/nextflow/src/test/groovy/nextflow/cli/module/CmdModuleInstallTest.groovy b/modules/nextflow/src/test/groovy/nextflow/cli/module/CmdModuleInstallTest.groovy
index c04dad81bb..a2f088b544 100644
--- a/modules/nextflow/src/test/groovy/nextflow/cli/module/CmdModuleInstallTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/cli/module/CmdModuleInstallTest.groovy
@@ -20,6 +20,7 @@ import io.seqera.npr.api.schema.v1.Module
 import io.seqera.npr.api.schema.v1.ModuleRelease
 import nextflow.cli.Launcher
 import nextflow.exception.AbortOperationException
+import nextflow.module.ModuleChecksum
 import nextflow.module.ModuleRegistryClient
 import nextflow.pipeline.PipelineSpec
 import org.apache.commons.compress.archivers.tar.TarArchiveEntry
@@ -61,11 +62,11 @@ class CmdModuleInstallTest extends Specification {
 
         // Mock registry client
         def mockClient = Mock(ModuleRegistryClient)
-        mockClient.fetchModule('@nf-core/fastqc') >> new Module(
-            name: '@nf-core/fastqc',
+        mockClient.fetchModule('nf-core/fastqc') >> new Module(
+            name: 'nf-core/fastqc',
             latest: new ModuleRelease(version: '1.0.0')
         )
-        mockClient.downloadModule('@nf-core/fastqc', '1.0.0', _) >> { String name, String version, Path dest ->
+        mockClient.downloadModule('nf-core/fastqc', '1.0.0', _) >> { String name, String version, Path dest ->
             Files.write(dest, modulePackage)
             return dest
         }
@@ -81,14 +82,14 @@ class CmdModuleInstallTest extends Specification {
         output.contains('1.0.0')
 
         and:
-        def moduleDir = tempDir.resolve('modules/@nf-core/fastqc')
+        def moduleDir = tempDir.resolve('modules/nf-core/fastqc')
         Files.exists(moduleDir)
         Files.exists(moduleDir.resolve('main.nf'))
         Files.exists(moduleDir.resolve('meta.yml'))
 
         and:
         def spec = new PipelineSpec(tempDir)
-        spec.getModules().get('@nf-core/fastqc') == '1.0.0'
+        spec.getModules().get('nf-core/fastqc') == '1.0.0'
     }
 
     def 'should install module with specific version'() {
@@ -122,14 +123,14 @@ class CmdModuleInstallTest extends Specification {
 
         and:
         def spec = new PipelineSpec(tempDir)
-        spec.getModules().get('@nf-core/fastqc') == '2.0.0'
+        spec.getModules().get('nf-core/fastqc') == '2.0.0'
 
     }
 
     def 'should update existing module with force flag'() {
         given:
         // Pre-install version 1.0.0
-        def moduleDir = tempDir.resolve('modules/@nf-core/fastqc')
+        def moduleDir = tempDir.resolve('modules/nf-core/fastqc')
         Files.createDirectories(moduleDir)
         moduleDir.resolve('main.nf').text = 'process OLD { }'
         moduleDir.resolve('meta.yml').text = """
@@ -139,7 +140,7 @@ class CmdModuleInstallTest extends Specification {
                                                     """.stripIndent()
 
         def spec = new PipelineSpec(tempDir)
-        spec.addModuleEntry('@nf-core/fastqc', '1.0.0')
+        spec.addModuleEntry('nf-core/fastqc', '1.0.0')
 
         and:
         def cmd = new CmdModuleInstall()
@@ -155,7 +156,7 @@ class CmdModuleInstallTest extends Specification {
         def modulePackage = createModulePackage('nf-core', 'fastqc', '2.0.0')
 
         def mockClient = Mock(ModuleRegistryClient)
-        mockClient.downloadModule('@nf-core/fastqc', '2.0.0', _) >> { String name, String version, Path dest ->
+        mockClient.downloadModule('nf-core/fastqc', '2.0.0', _) >> { String name, String version, Path dest ->
             Files.write(dest, modulePackage)
             return dest
         }
@@ -171,7 +172,7 @@ class CmdModuleInstallTest extends Specification {
 
         and:
         def updatedSpec = new PipelineSpec(tempDir)
-        updatedSpec.getModules().get('@nf-core/fastqc') == '2.0.0'
+        updatedSpec.getModules().get('nf-core/fastqc') == '2.0.0'
 
         and:
         moduleDir.resolve('main.nf').text.contains('FASTQC')  // New content
@@ -180,7 +181,7 @@ class CmdModuleInstallTest extends Specification {
     def 'should fail when module already installed without force'() {
         given:
         // Pre-install the module
-        def moduleDir = tempDir.resolve('modules/@nf-core/fastqc')
+        def moduleDir = tempDir.resolve('modules/nf-core/fastqc')
         Files.createDirectories(moduleDir)
         moduleDir.resolve('main.nf').text = 'process FASTQC { }'
         moduleDir.resolve('meta.yml').text = """
@@ -188,9 +189,9 @@ class CmdModuleInstallTest extends Specification {
                                                     version: '1.0.0'
                                                     description: Test module
                                                     """.stripIndent()
-        moduleDir.resolve('.checksum').text = 'wrong-checksum'
+        ModuleChecksum.save(moduleDir, 'wrong-checksum')
         def spec = new PipelineSpec(tempDir)
-        spec.addModuleEntry('@nf-core/fastqc', '1.0.0')
+        spec.addModuleEntry('nf-core/fastqc', '1.0.0')
 
         and:
         def cmd = new CmdModuleInstall()
@@ -202,8 +203,8 @@ class CmdModuleInstallTest extends Specification {
         cmd.root = tempDir
 
         def mockClient = Mock(ModuleRegistryClient)
-        mockClient.fetchModule('@nf-core/fastqc') >> new Module(
-            name: '@nf-core/fastqc',
+        mockClient.fetchModule('nf-core/fastqc') >> new Module(
+            name: 'nf-core/fastqc',
             latest: new ModuleRelease(version: '2.0.0')
         )
         cmd.client = mockClient
@@ -229,11 +230,11 @@ class CmdModuleInstallTest extends Specification {
         def modulePackage = createModulePackage('myorg', 'custom-module', '1.0.0')
 
         def mockClient = Mock(ModuleRegistryClient)
-        mockClient.fetchModule('@myorg/custom-module') >> new Module(
-            name: '@myorg/custom-module',
+        mockClient.fetchModule('myorg/custom-module') >> new Module(
+            name: 'myorg/custom-module',
             latest: new ModuleRelease(version: '1.0.0')
         )
-        mockClient.downloadModule('@myorg/custom-module', '1.0.0', _) >> { String name, String version, Path dest ->
+        mockClient.downloadModule('myorg/custom-module', '1.0.0', _) >> { String name, String version, Path dest ->
             Files.write(dest, modulePackage)
             return dest
         }
@@ -243,13 +244,13 @@ class CmdModuleInstallTest extends Specification {
         cmd.run()
 
         then:
-        def moduleDir = tempDir.resolve('modules/@myorg/custom-module')
+        def moduleDir = tempDir.resolve('modules/myorg/custom-module')
         Files.exists(moduleDir)
         Files.exists(moduleDir.resolve('main.nf'))
 
         and:
         def spec = new PipelineSpec(tempDir)
-        spec.getModules().get('@myorg/custom-module') == '1.0.0'
+        spec.getModules().get('myorg/custom-module') == '1.0.0'
     }
 
     def 'should create modules directory if it does not exist'() {
@@ -265,11 +266,11 @@ class CmdModuleInstallTest extends Specification {
         def modulePackage = createModulePackage('nf-core', 'fastqc', '1.0.0')
 
         def mockClient = Mock(ModuleRegistryClient)
-        mockClient.fetchModule('@nf-core/fastqc') >> new Module(
+        mockClient.fetchModule('nf-core/fastqc') >> new Module(
             name: 'nf-core/fastqc',
             latest: new ModuleRelease(version: '1.0.0')
         )
-        mockClient.downloadModule('@nf-core/fastqc', '1.0.0', _) >> { String name, String version, Path dest ->
+        mockClient.downloadModule('nf-core/fastqc', '1.0.0', _) >> { String name, String version, Path dest ->
             Files.write(dest, modulePackage)
             return dest
         }
@@ -280,8 +281,8 @@ class CmdModuleInstallTest extends Specification {
 
         then:
         Files.exists(tempDir.resolve('modules'))
-        Files.exists(tempDir.resolve('modules/@nf-core'))
-        Files.exists(tempDir.resolve('modules/@nf-core/fastqc'))
+        Files.exists(tempDir.resolve('modules/nf-core'))
+        Files.exists(tempDir.resolve('modules/nf-core/fastqc'))
     }
 
     def 'should create checksum file after installation'() {
@@ -297,11 +298,11 @@ class CmdModuleInstallTest extends Specification {
         def modulePackage = createModulePackage('nf-core', 'fastqc', '1.0.0')
 
         def mockClient = Mock(ModuleRegistryClient)
-        mockClient.fetchModule('@nf-core/fastqc') >> new Module(
+        mockClient.fetchModule('nf-core/fastqc') >> new Module(
             name: 'nf-core/fastqc',
             latest: new ModuleRelease(version: '1.0.0')
         )
-        mockClient.downloadModule('@nf-core/fastqc', '1.0.0', _) >> { String name, String version, Path dest ->
+        mockClient.downloadModule('nf-core/fastqc', '1.0.0', _) >> { String name, String version, Path dest ->
             Files.write(dest, modulePackage)
             return dest
         }
@@ -311,11 +312,11 @@ class CmdModuleInstallTest extends Specification {
         cmd.run()
 
         then:
-        def moduleDir = tempDir.resolve('modules/@nf-core/fastqc')
-        Files.exists(moduleDir.resolve('.checksum'))
+        def moduleDir = tempDir.resolve('modules/nf-core/fastqc')
+        Files.exists(moduleDir.resolve('.module-info'))
 
         and:
-        def checksum = moduleDir.resolve('.checksum').text
+        def checksum = ModuleChecksum.load(moduleDir)
         checksum != null
         !checksum.isEmpty()
     }
diff --git a/modules/nextflow/src/test/groovy/nextflow/cli/module/CmdModuleListTest.groovy b/modules/nextflow/src/test/groovy/nextflow/cli/module/CmdModuleListTest.groovy
index 8d745562a3..00bafc75b8 100644
--- a/modules/nextflow/src/test/groovy/nextflow/cli/module/CmdModuleListTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/cli/module/CmdModuleListTest.groovy
@@ -65,7 +65,7 @@ class CmdModuleListTest extends Specification {
         output.contains('1.0.0')
         output.contains('nf-core/multiqc')
         output.contains('2.1.0')
-        output.contains('OK') || output.contains('NO CHECKSUM')
+        output.contains('OK')
     }
 
     def 'should list installed modules with JSON output'() {
@@ -177,9 +177,8 @@ class CmdModuleListTest extends Specification {
             description: Test module
         """.stripIndent()
 
-        // Create checksum
-        def checksum = ModuleChecksum.compute(moduleDir)
-        moduleDir.resolve('.checksum').text = checksum
+        // Create .module-info
+        ModuleChecksum.save(moduleDir, ModuleChecksum.compute(moduleDir))
 
         return moduleDir
     }
diff --git a/modules/nextflow/src/test/groovy/nextflow/cli/module/CmdModuleRemoveTest.groovy b/modules/nextflow/src/test/groovy/nextflow/cli/module/CmdModuleRemoveTest.groovy
index 0361b3a274..0b4972c3ef 100644
--- a/modules/nextflow/src/test/groovy/nextflow/cli/module/CmdModuleRemoveTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/cli/module/CmdModuleRemoveTest.groovy
@@ -51,7 +51,7 @@ class CmdModuleRemoveTest extends Specification {
 
         // Create spec file with module entry
         def specFile = new PipelineSpec(tempDir)
-        specFile.addModuleEntry('@nf-core/fastqc', '1.0.0')
+        specFile.addModuleEntry('nf-core/fastqc', '1.0.0')
 
         and:
         def cmd = new CmdModuleRemove()
@@ -71,7 +71,7 @@ class CmdModuleRemoveTest extends Specification {
 
         and:
         def spec = new PipelineSpec(tempDir)
-        spec.getModules().get('@nf-core/fastqc') == null
+        spec.getModules().get('nf-core/fastqc') == null
     }
 
     def 'should keep config with -keep-config flag'() {
@@ -82,7 +82,7 @@ class CmdModuleRemoveTest extends Specification {
 
         // Create spec file
         def specFile = new PipelineSpec(tempDir)
-        specFile.addModuleEntry('@nf-core/fastqc', '1.0.0')
+        specFile.addModuleEntry('nf-core/fastqc', '1.0.0')
 
         and:
         def cmd = new CmdModuleRemove()
@@ -101,7 +101,7 @@ class CmdModuleRemoveTest extends Specification {
 
         and:
         def spec = new PipelineSpec(tempDir)
-        spec.getModules().get('@nf-core/fastqc') == '1.0.0'
+        spec.getModules().get('nf-core/fastqc') == '1.0.0'
     }
 
     def 'should keep files with -keep-files flag'() {
@@ -112,7 +112,7 @@ class CmdModuleRemoveTest extends Specification {
 
         // Create spec file
         def specFile = new PipelineSpec(tempDir)
-        specFile.addModuleEntry('@nf-core/fastqc', '1.0.0')
+        specFile.addModuleEntry('nf-core/fastqc', '1.0.0')
 
         and:
         def cmd = new CmdModuleRemove()
@@ -132,7 +132,7 @@ class CmdModuleRemoveTest extends Specification {
 
         and:
         def spec = new PipelineSpec(tempDir)
-        spec.getModules().get('@nf-core/fastqc') == null
+        spec.getModules().get('nf-core/fastqc') == null
     }
 
     def 'should fail when both keep flags are set'() {
diff --git a/modules/nextflow/src/test/groovy/nextflow/cli/module/CmdModuleRunTest.groovy b/modules/nextflow/src/test/groovy/nextflow/cli/module/CmdModuleRunTest.groovy
index c3741d0fe1..d93f58be53 100644
--- a/modules/nextflow/src/test/groovy/nextflow/cli/module/CmdModuleRunTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/cli/module/CmdModuleRunTest.groovy
@@ -89,7 +89,7 @@ class CmdModuleRunTest extends Specification {
         def moduleRelease = new ModuleRelease()
         moduleRelease.version = '1.0.0'
         def module = new Module()
-        module.name = '@nf-core/test-module'
+        module.name = 'nf-core/test-module'
         module.latest = moduleRelease
         mockClient.fetchModule(_) >> module  // Use wildcard to match any argument
         mockClient.downloadModule(_, _, _) >> { String name, String version, Path dest ->
@@ -152,7 +152,7 @@ class CmdModuleRunTest extends Specification {
         def modulePackage = createModulePackage(moduleScript)
 
         def mockClient = Mock(ModuleRegistryClient)
-        mockClient.downloadModule('@nf-core/test-module', '2.0.0', _) >> { String name, String version, Path dest ->
+        mockClient.downloadModule('nf-core/test-module', '2.0.0', _) >> { String name, String version, Path dest ->
             Files.write(dest, modulePackage)
             return dest
         }
diff --git a/modules/nextflow/src/test/groovy/nextflow/config/ModulesConfigTest.groovy b/modules/nextflow/src/test/groovy/nextflow/config/ModulesConfigTest.groovy
index d4c28cbf6f..f320aa472d 100644
--- a/modules/nextflow/src/test/groovy/nextflow/config/ModulesConfigTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/config/ModulesConfigTest.groovy
@@ -38,11 +38,11 @@ class ModulesConfigTest extends Specification {
         def config = new ModulesConfig()
 
         when:
-        config.setVersion('@nf-core/fastqc', '1.0.0')
+        config.setVersion('nf-core/fastqc', '1.0.0')
 
         then:
-        config.getVersion('@nf-core/fastqc') == '1.0.0'
-        config.hasVersion('@nf-core/fastqc')
+        config.getVersion('nf-core/fastqc') == '1.0.0'
+        config.hasVersion('nf-core/fastqc')
     }
 
     def 'should return null for unconfigured module'() {
@@ -50,33 +50,33 @@ class ModulesConfigTest extends Specification {
         def config = new ModulesConfig()
 
         when:
-        def version = config.getVersion('@nf-core/bwa')
+        def version = config.getVersion('nf-core/bwa')
 
         then:
         version == null
-        !config.hasVersion('@nf-core/bwa')
+        !config.hasVersion('nf-core/bwa')
     }
 
     def 'should override existing version'() {
         given:
         def config = new ModulesConfig()
-        config.setVersion('@nf-core/fastqc', '1.0.0')
+        config.setVersion('nf-core/fastqc', '1.0.0')
 
         when:
-        config.setVersion('@nf-core/fastqc', '2.0.0')
+        config.setVersion('nf-core/fastqc', '2.0.0')
 
         then:
-        config.getVersion('@nf-core/fastqc') == '2.0.0'
+        config.getVersion('nf-core/fastqc') == '2.0.0'
     }
 
     def 'should return unmodifiable map from getModules'() {
         given:
         def config = new ModulesConfig()
-        config.setVersion('@nf-core/fastqc', '1.0.0')
+        config.setVersion('nf-core/fastqc', '1.0.0')
 
         when:
         def modules = config.getAllModules()
-        modules.put('@nf-core/bwa', '2.0.0')
+        modules.put('nf-core/bwa', '2.0.0')
 
         then:
         thrown(UnsupportedOperationException)
@@ -85,18 +85,18 @@ class ModulesConfigTest extends Specification {
     def 'should return all configured modules'() {
         given:
         def config = new ModulesConfig()
-        config.setVersion('@nf-core/fastqc', '1.0.0')
-        config.setVersion('@nf-core/bwa', '2.0.0')
-        config.setVersion('@myorg/custom', '0.5.0')
+        config.setVersion('nf-core/fastqc', '1.0.0')
+        config.setVersion('nf-core/bwa', '2.0.0')
+        config.setVersion('myorg/custom', '0.5.0')
 
         when:
         def modules = config.getAllModules()
 
         then:
         modules.size() == 3
-        modules['@nf-core/fastqc'] == '1.0.0'
-        modules['@nf-core/bwa'] == '2.0.0'
-        modules['@myorg/custom'] == '0.5.0'
+        modules['nf-core/fastqc'] == '1.0.0'
+        modules['nf-core/bwa'] == '2.0.0'
+        modules['myorg/custom'] == '0.5.0'
     }
 
     def 'should handle empty initialization'() {
@@ -105,7 +105,7 @@ class ModulesConfigTest extends Specification {
 
         then:
         config.getAllModules().isEmpty()
-        !config.hasVersion('@nf-core/fastqc')
+        !config.hasVersion('nf-core/fastqc')
     }
 
     def 'should store multiple versions independently'() {
@@ -113,14 +113,14 @@ class ModulesConfigTest extends Specification {
         def config = new ModulesConfig()
 
         when:
-        config.setVersion('@nf-core/fastqc', '1.0.0')
-        config.setVersion('@nf-core/bwa', '2.0.0')
-        config.setVersion('@myorg/custom', '0.5.0')
+        config.setVersion('nf-core/fastqc', '1.0.0')
+        config.setVersion('nf-core/bwa', '2.0.0')
+        config.setVersion('myorg/custom', '0.5.0')
 
         then:
-        config.getVersion('@nf-core/fastqc') == '1.0.0'
-        config.getVersion('@nf-core/bwa') == '2.0.0'
-        config.getVersion('@myorg/custom') == '0.5.0'
+        config.getVersion('nf-core/fastqc') == '1.0.0'
+        config.getVersion('nf-core/bwa') == '2.0.0'
+        config.getVersion('myorg/custom') == '0.5.0'
         config.allModules.size() == 3
     }
 
@@ -129,13 +129,13 @@ class ModulesConfigTest extends Specification {
         def config = new ModulesConfig()
 
         when:
-        config.setVersion('@org-name/module-name', '1.0.0')
-        config.setVersion('@org_name/module_name', '2.0.0')
+        config.setVersion('org-name/module-name', '1.0.0')
+        config.setVersion('org_name/module_name', '2.0.0')
         config.setVersion('simple-module', '3.0.0')
 
         then:
-        config.getVersion('@org-name/module-name') == '1.0.0'
-        config.getVersion('@org_name/module_name') == '2.0.0'
+        config.getVersion('org-name/module-name') == '1.0.0'
+        config.getVersion('org_name/module_name') == '2.0.0'
         config.getVersion('simple-module') == '3.0.0'
     }
 
@@ -144,41 +144,41 @@ class ModulesConfigTest extends Specification {
         def config = new ModulesConfig()
 
         when:
-        config.setVersion('@nf-core/fastqc', '1.0.0')
-        config.setVersion('@nf-core/bwa', 'v2.0.0')
-        config.setVersion('@nf-core/samtools', '1.0.0-beta')
-        config.setVersion('@nf-core/bowtie', '1.0.0-rc.1')
+        config.setVersion('nf-core/fastqc', '1.0.0')
+        config.setVersion('nf-core/bwa', 'v2.0.0')
+        config.setVersion('nf-core/samtools', '1.0.0-beta')
+        config.setVersion('nf-core/bowtie', '1.0.0-rc.1')
 
         then:
-        config.getVersion('@nf-core/fastqc') == '1.0.0'
-        config.getVersion('@nf-core/bwa') == 'v2.0.0'
-        config.getVersion('@nf-core/samtools') == '1.0.0-beta'
-        config.getVersion('@nf-core/bowtie') == '1.0.0-rc.1'
+        config.getVersion('nf-core/fastqc') == '1.0.0'
+        config.getVersion('nf-core/bwa') == 'v2.0.0'
+        config.getVersion('nf-core/samtools') == '1.0.0-beta'
+        config.getVersion('nf-core/bowtie') == '1.0.0-rc.1'
     }
 
     def 'should check if multiple modules have versions'() {
         given:
         def config = new ModulesConfig()
-        config.setVersion('@nf-core/fastqc', '1.0.0')
-        config.setVersion('@nf-core/bwa', '2.0.0')
+        config.setVersion('nf-core/fastqc', '1.0.0')
+        config.setVersion('nf-core/bwa', '2.0.0')
 
         expect:
-        config.hasVersion('@nf-core/fastqc')
-        config.hasVersion('@nf-core/bwa')
-        !config.hasVersion('@nf-core/samtools')
+        config.hasVersion('nf-core/fastqc')
+        config.hasVersion('nf-core/bwa')
+        !config.hasVersion('nf-core/samtools')
     }
 
     def 'should handle version updates'() {
         given:
         def config = new ModulesConfig()
-        config.setVersion('@nf-core/fastqc', '1.0.0')
+        config.setVersion('nf-core/fastqc', '1.0.0')
 
         when:
-        config.setVersion('@nf-core/fastqc', '1.1.0')
-        config.setVersion('@nf-core/fastqc', '2.0.0')
+        config.setVersion('nf-core/fastqc', '1.1.0')
+        config.setVersion('nf-core/fastqc', '2.0.0')
 
         then:
-        config.getVersion('@nf-core/fastqc') == '2.0.0'
+        config.getVersion('nf-core/fastqc') == '2.0.0'
     }
 
     def 'should maintain separate versions for different modules'() {
@@ -186,12 +186,12 @@ class ModulesConfigTest extends Specification {
         def config = new ModulesConfig()
 
         when:
-        config.setVersion('@nf-core/fastqc', '1.0.0')
-        config.setVersion('@nf-core/bwa', '2.0.0')
+        config.setVersion('nf-core/fastqc', '1.0.0')
+        config.setVersion('nf-core/bwa', '2.0.0')
 
         then:
-        config.getVersion('@nf-core/fastqc') == '1.0.0'
-        config.getVersion('@nf-core/bwa') == '2.0.0'
-        config.getVersion('@nf-core/fastqc') != config.getVersion('@nf-core/bwa')
+        config.getVersion('nf-core/fastqc') == '1.0.0'
+        config.getVersion('nf-core/bwa') == '2.0.0'
+        config.getVersion('nf-core/fastqc') != config.getVersion('nf-core/bwa')
     }
 }
diff --git a/modules/nextflow/src/test/groovy/nextflow/module/InstalledModuleTest.groovy b/modules/nextflow/src/test/groovy/nextflow/module/InstalledModuleTest.groovy
index 850466ab48..e526dde81f 100644
--- a/modules/nextflow/src/test/groovy/nextflow/module/InstalledModuleTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/module/InstalledModuleTest.groovy
@@ -60,7 +60,7 @@ class InstalledModuleTest extends Specification {
             directory: moduleDir,
             mainFile: mainFile,
             manifestFile: metaFile,
-            checksumFile: moduleDir.resolve('.checksum'),
+            moduleInfoFile: moduleDir.resolve('.module-info'),
             expectedChecksum: actualChecksum,
             installedVersion: "0.0.1"
         )
@@ -95,7 +95,7 @@ class InstalledModuleTest extends Specification {
             directory: moduleDir,
             mainFile: mainFile,
             manifestFile: metaFile,
-            checksumFile: moduleDir.resolve('.checksum'),
+            moduleInfoFile: moduleDir.resolve('.module-info'),
             expectedChecksum: originalChecksum,
             installedVersion: "0.0.1"
         )
@@ -118,15 +118,15 @@ class InstalledModuleTest extends Specification {
         def metaFile = moduleDir.resolve('meta.yml')
         metaFile.text = 'name: test/module\nversion: 0.0.1'
 
-        def checksumFile = moduleDir.resolve('.checksum')
-        checksumFile.text = 'some-checksum'
+        def moduleInfoFile = moduleDir.resolve('.module-info')
+        // CORRUPTED check happens before .module-info check, so content doesn't matter here
 
         def installed = new InstalledModule(
             reference: new ModuleReference('test', 'module'),
             directory: moduleDir,
             mainFile: mainFile,
             manifestFile: metaFile,
-            checksumFile: checksumFile,
+            moduleInfoFile: moduleInfoFile,
             expectedChecksum: 'some-checksum'
         )
 
@@ -137,7 +137,7 @@ class InstalledModuleTest extends Specification {
         integrity == ModuleIntegrity.CORRUPTED
     }
 
-    def 'should report MISSING_CHECKSUM when checksum file absent'() {
+    def 'should report NO_REMOTE_MODULE when .module-info file absent'() {
         given:
         def moduleDir = tempDir.resolve('module')
         Files.createDirectories(moduleDir)
@@ -148,15 +148,15 @@ class InstalledModuleTest extends Specification {
         def metaFile = moduleDir.resolve('meta.yml')
         metaFile.text = 'name: test/module\nversion: 0.0.1'
 
-        def checksumFile = moduleDir.resolve('.checksum')
-        // Don't create checksum file
+        def moduleInfoFile = moduleDir.resolve('.module-info')
+        // Don't create .module-info file
 
         def installed = new InstalledModule(
             reference: new ModuleReference('test', 'module'),
             directory: moduleDir,
             mainFile: mainFile,
             manifestFile: metaFile,
-            checksumFile: checksumFile,
+            moduleInfoFile: moduleInfoFile,
             expectedChecksum: null
         )
 
@@ -164,7 +164,7 @@ class InstalledModuleTest extends Specification {
         def integrity = installed.getIntegrity()
 
         then:
-        integrity == ModuleIntegrity.MISSING_CHECKSUM
+        integrity == ModuleIntegrity.NO_REMOTE_MODULE
     }
 
     def 'should handle checksum computation failure gracefully'() {
@@ -178,16 +178,16 @@ class InstalledModuleTest extends Specification {
         def metaFile = moduleDir.resolve('meta.yml')
         metaFile.text = 'name: test/module\nversion: 0.0.1'
 
-        // Create checksum file with a value that won't match the computed checksum
-        def checksumFile = moduleDir.resolve('.checksum')
-        checksumFile.text = 'expected-checksum-that-will-not-match'
+        // Create .module-info with a checksum that won't match the computed checksum
+        ModuleChecksum.save(moduleDir, 'expected-checksum-that-will-not-match')
+        def moduleInfoFile = moduleDir.resolve('.module-info')
 
         def installed = new InstalledModule(
             reference: new ModuleReference('test', 'module'),
             directory: moduleDir,
             mainFile: mainFile,
             manifestFile: metaFile,
-            checksumFile: checksumFile,
+            moduleInfoFile: moduleInfoFile,
             expectedChecksum: 'expected-checksum-that-will-not-match'
         )
 
diff --git a/modules/nextflow/src/test/groovy/nextflow/module/ModuleChecksumTest.groovy b/modules/nextflow/src/test/groovy/nextflow/module/ModuleChecksumTest.groovy
index 31c6600373..4bb9185681 100644
--- a/modules/nextflow/src/test/groovy/nextflow/module/ModuleChecksumTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/module/ModuleChecksumTest.groovy
@@ -97,7 +97,7 @@ class ModuleChecksumTest extends Specification {
         checksum1 != checksum2
     }
 
-    def 'should exclude .checksum file from computation'() {
+    def 'should exclude .module-info file from computation'() {
         given:
         def moduleDir = tempDir.resolve('module')
         Files.createDirectories(moduleDir)
@@ -107,14 +107,14 @@ class ModuleChecksumTest extends Specification {
         // Compute initial checksum
         def checksum1 = ModuleChecksum.compute(moduleDir)
 
-        // Add .checksum file
-        moduleDir.resolve('.checksum').text = 'some-checksum-value'
+        // Add .module-info file
+        ModuleChecksum.save(moduleDir, 'some-checksum-value')
 
         // Compute checksum again
         def checksum2 = ModuleChecksum.compute(moduleDir)
 
         expect:
-        checksum1 == checksum2  // Should be the same, .checksum is ignored
+        checksum1 == checksum2  // Should be the same, .module-info is ignored
     }
 
     def 'should include subdirectories in checksum'() {
@@ -139,7 +139,7 @@ class ModuleChecksumTest extends Specification {
         checksum1 != checksum2  // Checksums should differ
     }
 
-    def 'should save checksum to .checksum file'() {
+    def 'should save checksum to .module-info file'() {
         given:
         def moduleDir = tempDir.resolve('module')
         Files.createDirectories(moduleDir)
@@ -149,17 +149,16 @@ class ModuleChecksumTest extends Specification {
         ModuleChecksum.save(moduleDir, checksumValue)
 
         then:
-        def checksumFile = moduleDir.resolve('.checksum')
-        Files.exists(checksumFile)
-        checksumFile.text.trim() == checksumValue
+        def moduleInfoFile = moduleDir.resolve('.module-info')
+        Files.exists(moduleInfoFile)
+        ModuleChecksum.load(moduleDir) == checksumValue
     }
 
-    def 'should load checksum from .checksum file'() {
+    def 'should load checksum from .module-info file'() {
         given:
         def moduleDir = tempDir.resolve('module')
         Files.createDirectories(moduleDir)
-        def checksumFile = moduleDir.resolve('.checksum')
-        checksumFile.text = 'abc123def456'
+        ModuleChecksum.save(moduleDir, 'abc123def456')
 
         when:
         def checksum = ModuleChecksum.load(moduleDir)
diff --git a/modules/nextflow/src/test/groovy/nextflow/module/ModuleReferenceTest.groovy b/modules/nextflow/src/test/groovy/nextflow/module/ModuleReferenceTest.groovy
index 64b0613be8..b906b83c9f 100644
--- a/modules/nextflow/src/test/groovy/nextflow/module/ModuleReferenceTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/module/ModuleReferenceTest.groovy
@@ -26,34 +26,32 @@ import spock.lang.Specification
  */
 class ModuleReferenceTest extends Specification {
 
-    def 'should parse valid module reference with @'() {
+    def 'should parse valid module reference without @'() {
         when:
-        def ref = ModuleReference.parse('@nf-core/fastqc')
+        def ref = ModuleReference.parse('nf-core/fastqc')
 
         then:
         ref.scope == 'nf-core'
         ref.name == 'fastqc'
-        ref.fullName == '@nf-core/fastqc'
+        ref.fullName == 'nf-core/fastqc'
     }
 
-    def 'should parse valid module reference without @'() {
+    def 'should reject module reference with @ prefix'() {
         when:
-        def ref = ModuleReference.parse('nf-core/fastqc')
+        ModuleReference.parse('@nf-core/fastqc')
 
         then:
-        ref.scope == 'nf-core'
-        ref.name == 'fastqc'
-        ref.fullName == '@nf-core/fastqc'
+        thrown(AbortOperationException)
     }
 
     def 'should parse module reference with multiple slashes'() {
         when:
-        def ref = ModuleReference.parse('@myorg/samtools/view')
+        def ref = ModuleReference.parse('myorg/samtools/view')
 
         then:
         ref.scope == 'myorg'
         ref.name == 'samtools/view'
-        ref.fullName == '@myorg/samtools/view'
+        ref.fullName == 'myorg/samtools/view'
     }
 
     def 'should reject invalid module reference without scope'() {
@@ -80,7 +78,7 @@ class ModuleReferenceTest extends Specification {
         thrown(AbortOperationException)
     }
 
-    def 'should reject module reference with only @'() {
+    def 'should reject bare @ character'() {
         when:
         ModuleReference.parse('@')
 
@@ -90,15 +88,15 @@ class ModuleReferenceTest extends Specification {
 
     def 'should reject module reference with only scope'() {
         when:
-        ModuleReference.parse('@nf-core/')
+        ModuleReference.parse('nf-core/')
 
         then:
         thrown(AbortOperationException)
     }
 
-    def 'should handle module reference with trailing slash'() {
+    def 'should reject module reference with trailing slash'() {
         when:
-        ModuleReference.parse('@nf-core/fastqc/')
+        ModuleReference.parse('nf-core/fastqc/')
 
         then:
         thrown(AbortOperationException)
@@ -111,12 +109,12 @@ class ModuleReferenceTest extends Specification {
         then:
         ref.scope == 'nf-core'
         ref.name == 'fastqc'
-        ref.fullName == '@nf-core/fastqc'
+        ref.fullName == 'nf-core/fastqc'
     }
 
     def 'should handle scope names with hyphens'() {
         when:
-        def ref = ModuleReference.parse('@my-org/my-module')
+        def ref = ModuleReference.parse('my-org/my-module')
 
         then:
         ref.scope == 'my-org'
@@ -125,7 +123,7 @@ class ModuleReferenceTest extends Specification {
 
     def 'should handle scope names with underscores'() {
         when:
-        def ref = ModuleReference.parse('@my_org/my_module')
+        def ref = ModuleReference.parse('my_org/my_module')
 
         then:
         ref.scope == 'my_org'
@@ -134,7 +132,7 @@ class ModuleReferenceTest extends Specification {
 
     def 'should handle module names with numbers'() {
         when:
-        def ref = ModuleReference.parse('@nf-core/bwa-mem2')
+        def ref = ModuleReference.parse('nf-core/bwa-mem2')
 
         then:
         ref.scope == 'nf-core'
@@ -143,9 +141,9 @@ class ModuleReferenceTest extends Specification {
 
     def 'should implement equals correctly'() {
         given:
-        def ref1 = ModuleReference.parse('@nf-core/fastqc')
-        def ref2 = ModuleReference.parse('@nf-core/fastqc')
-        def ref3 = ModuleReference.parse('@nf-core/multiqc')
+        def ref1 = ModuleReference.parse('nf-core/fastqc')
+        def ref2 = ModuleReference.parse('nf-core/fastqc')
+        def ref3 = ModuleReference.parse('nf-core/multiqc')
 
         expect:
         ref1 == ref2
@@ -154,8 +152,8 @@ class ModuleReferenceTest extends Specification {
 
     def 'should implement hashCode correctly'() {
         given:
-        def ref1 = ModuleReference.parse('@nf-core/fastqc')
-        def ref2 = ModuleReference.parse('@nf-core/fastqc')
+        def ref1 = ModuleReference.parse('nf-core/fastqc')
+        def ref2 = ModuleReference.parse('nf-core/fastqc')
 
         expect:
         ref1.hashCode() == ref2.hashCode()
@@ -163,17 +161,17 @@ class ModuleReferenceTest extends Specification {
 
     def 'should implement toString correctly'() {
         given:
-        def ref = ModuleReference.parse('@nf-core/fastqc')
+        def ref = ModuleReference.parse('nf-core/fastqc')
 
         expect:
-        ref.toString() == '@nf-core/fastqc'
+        ref.toString() == 'nf-core/fastqc'
     }
 
     def 'should be usable as map key'() {
         given:
-        def ref1 = ModuleReference.parse('@nf-core/fastqc')
-        def ref2 = ModuleReference.parse('@nf-core/fastqc')
-        def ref3 = ModuleReference.parse('@nf-core/multiqc')
+        def ref1 = ModuleReference.parse('nf-core/fastqc')
+        def ref2 = ModuleReference.parse('nf-core/fastqc')
+        def ref3 = ModuleReference.parse('nf-core/multiqc')
 
         def map = [:]
         map[ref1] = 'value1'
@@ -187,7 +185,7 @@ class ModuleReferenceTest extends Specification {
 
     def 'should handle org-style scopes'() {
         when:
-        def ref = ModuleReference.parse('@mycompany.io/custom-module')
+        def ref = ModuleReference.parse('mycompany.io/custom-module')
 
         then:
         ref.scope == 'mycompany.io'
@@ -196,7 +194,7 @@ class ModuleReferenceTest extends Specification {
 
     def 'should reject module reference with spaces'() {
         when:
-        ModuleReference.parse('@nf-core/fast qc')
+        ModuleReference.parse('nf-core/fast qc')
 
         then:
         thrown(AbortOperationException)
@@ -204,7 +202,7 @@ class ModuleReferenceTest extends Specification {
 
     def 'should reject module reference with special characters'() {
         when:
-        ModuleReference.parse('@nf-core/fastqc!')
+        ModuleReference.parse('nf-core/fastqc!')
 
         then:
         thrown(AbortOperationException)
@@ -212,17 +210,17 @@ class ModuleReferenceTest extends Specification {
 
     def 'should handle deeply nested module names'() {
         when:
-        def ref = ModuleReference.parse('@nf-core/samtools/sort/parallel')
+        def ref = ModuleReference.parse('nf-core/samtools/sort/parallel')
 
         then:
         ref.scope == 'nf-core'
         ref.name == 'samtools/sort/parallel'
-        ref.fullName == '@nf-core/samtools/sort/parallel'
+        ref.fullName == 'nf-core/samtools/sort/parallel'
     }
 
     def 'should parse from string with leading/trailing whitespace'() {
         when:
-        def ref = ModuleReference.parse('  @nf-core/fastqc  ')
+        def ref = ModuleReference.parse('  nf-core/fastqc  ')
 
         then:
         ref.scope == 'nf-core'
diff --git a/modules/nextflow/src/test/groovy/nextflow/module/ModuleResolverTest.groovy b/modules/nextflow/src/test/groovy/nextflow/module/ModuleResolverTest.groovy
index 8c145bb89c..ab959dfb57 100644
--- a/modules/nextflow/src/test/groovy/nextflow/module/ModuleResolverTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/module/ModuleResolverTest.groovy
@@ -88,7 +88,7 @@ class ModuleResolverTest extends Specification {
             name: nf-core/fastqc
             version: 1.0.0
         '''
-        moduleDir.resolve('.checksum').text = 'wrong-checksum'
+        ModuleChecksum.save(moduleDir, 'wrong-checksum')
 
         when:
         def result = resolver.resolve(reference, null, false)
@@ -103,7 +103,7 @@ class ModuleResolverTest extends Specification {
 
     def 'should throw exception when version mismatch without auto-install'() {
         given:
-        def modulesConfig = new ModulesConfig(['@nf-core/fastqc': '2.0.0'])
+        def modulesConfig = new ModulesConfig(['nf-core/fastqc': '2.0.0'])
         def resolver = new ModuleResolver(tempDir, modulesConfig, null)
         def reference = new ModuleReference('nf-core', 'fastqc')
         def storage = new ModuleStorage(tempDir)
@@ -119,7 +119,7 @@ class ModuleResolverTest extends Specification {
 
         // Compute and save correct checksum
         def checksum = ModuleChecksum.compute(moduleDir)
-        moduleDir.resolve('.checksum').text = checksum
+        ModuleChecksum.save(moduleDir, checksum)
 
         when:
         resolver.resolve(reference, null, false)
@@ -152,7 +152,7 @@ class ModuleResolverTest extends Specification {
 
         // Compute and save correct checksum
         def checksum = ModuleChecksum.compute(moduleDir)
-        moduleDir.resolve('.checksum').text = checksum
+        ModuleChecksum.save(moduleDir, checksum)
 
         when:
         def result = resolver.resolve(reference, '1.0.0', false)
@@ -178,7 +178,7 @@ class ModuleResolverTest extends Specification {
             name: nf-core/fastqc
             version: 1.0.0
         '''
-        moduleDir.resolve('.checksum').text = 'wrong-checksum'
+        ModuleChecksum.save(moduleDir, 'wrong-checksum')
 
         when:
         resolver.installModule(reference, '2.0.0', false)
diff --git a/modules/nextflow/src/test/groovy/nextflow/module/ModuleStorageTest.groovy b/modules/nextflow/src/test/groovy/nextflow/module/ModuleStorageTest.groovy
index dab9517ddc..258c4c354b 100644
--- a/modules/nextflow/src/test/groovy/nextflow/module/ModuleStorageTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/module/ModuleStorageTest.groovy
@@ -50,7 +50,7 @@ class ModuleStorageTest extends Specification {
         def moduleDir = storage.getModuleDir(reference)
 
         then:
-        moduleDir == tempDir.resolve('modules/@nf-core/fastqc')
+        moduleDir == tempDir.resolve('modules/nf-core/fastqc')
     }
 
     def 'should check if module is installed'() {
@@ -107,9 +107,9 @@ class ModuleStorageTest extends Specification {
               - fastqc
         '''.stripIndent()
 
-        // Create .checksum file
-        def checksumFile = moduleDir.resolve('.checksum')
-        checksumFile.text = 'abc123def456'
+        // Create .module-info file
+        ModuleChecksum.save(moduleDir, 'abc123def456')
+        def moduleInfoFile = moduleDir.resolve('.module-info')
 
         when:
         def installed = storage.getInstalledModule(reference)
@@ -120,7 +120,7 @@ class ModuleStorageTest extends Specification {
         installed.directory == moduleDir
         installed.mainFile == mainFile
         installed.manifestFile == moduleDir.resolve('meta.yml')
-        installed.checksumFile == checksumFile
+        installed.moduleInfoFile == moduleInfoFile
         installed.expectedChecksum == 'abc123def456'
         installed.installedVersion == '1.0.0'
     }
@@ -145,12 +145,12 @@ class ModuleStorageTest extends Specification {
 
             // Create meta.yml with version
             moduleDir.resolve('meta.yml').text = """
-                name: ${ref.nameWithoutPrefix}
+                name: ${ref}
                 version: 1.0.0
             """.stripIndent()
 
-            // Create .checksum
-            moduleDir.resolve('.checksum').text = 'checksum'
+            // Create .module-info
+            ModuleChecksum.save(moduleDir, 'checksum')
         }
 
         when:
@@ -158,7 +158,7 @@ class ModuleStorageTest extends Specification {
 
         then:
         installed.size() == 3
-        installed*.reference.fullName.sort() == ['@myorg/custom', '@nf-core/fastqc', '@nf-core/multiqc']
+        installed*.reference.fullName.sort() == ['myorg/custom', 'nf-core/fastqc', 'nf-core/multiqc']
     }
 
     def 'should list nested modules recursively'() {
@@ -182,14 +182,14 @@ class ModuleStorageTest extends Specification {
 
             // Create meta.yml with version
             moduleDir.resolve('meta.yml').text = """
-                name: ${ref.nameWithoutPrefix}
+                name: ${ref}
                 version: 1.0.0
                 description: Test module
                 license: MIT
             """.stripIndent()
 
-            // Create .checksum
-            moduleDir.resolve('.checksum').text = 'checksum'
+            // Create .module-info
+            ModuleChecksum.save(moduleDir, 'checksum')
         }
 
         when:
@@ -198,10 +198,10 @@ class ModuleStorageTest extends Specification {
         then:
         installed.size() == 4
         installed*.reference.fullName.sort() == [
-            '@myorg/tools/subtools/module',
-            '@nf-core/fastqc',
-            '@nf-core/gfatools/gfa2fa',
-            '@nf-core/gfatools/gfa2gfa'
+            'myorg/tools/subtools/module',
+            'nf-core/fastqc',
+            'nf-core/gfatools/gfa2fa',
+            'nf-core/gfatools/gfa2gfa'
         ]
     }
 
@@ -234,7 +234,7 @@ class ModuleStorageTest extends Specification {
         installed.reference == reference
         installed.installedVersion == '1.0.0'
         Files.exists(installed.mainFile)
-        Files.exists(installed.checksumFile)
+        Files.exists(installed.moduleInfoFile)
 
         cleanup:
         packageFile?.delete()
@@ -313,7 +313,7 @@ class ModuleStorageTest extends Specification {
         then:
         installed.expectedChecksum != null
         installed.expectedChecksum.length() > 0
-        Files.exists(installed.checksumFile)
+        Files.exists(installed.moduleInfoFile)
 
         cleanup:
         packageFile?.delete()
diff --git a/modules/nextflow/src/test/groovy/nextflow/script/IncludeDefTest.groovy b/modules/nextflow/src/test/groovy/nextflow/script/IncludeDefTest.groovy
index b5e1b7425e..527cbbfbbd 100644
--- a/modules/nextflow/src/test/groovy/nextflow/script/IncludeDefTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/script/IncludeDefTest.groovy
@@ -45,8 +45,8 @@ class IncludeDefTest extends Specification {
 
         expect:
         include.resolveModulePath('/abs/foo.nf') == '/abs/foo.nf' as Path
-        include.resolveModulePath('module.nf') == '/some/path/module.nf' as Path
-        include.resolveModulePath('foo/bar.nf') == '/some/path/foo/bar.nf' as Path
+        include.resolveModulePath('./module.nf') == '/some/path/module.nf' as Path
+        include.resolveModulePath('./foo/bar.nf') == '/some/path/foo/bar.nf' as Path
 
         when:
         include.resolveModulePath('http://foo.com/bar')
@@ -66,17 +66,17 @@ class IncludeDefTest extends Specification {
         include.getOwnerPath() >> script
 
         when:
-        def result = include.realModulePath( 'mod-x.nf')
+        def result = include.realModulePath( './mod-x.nf')
         then:
         result == module
 
         when:
-        result = include.realModulePath('mod-x')
+        result = include.realModulePath('./mod-x')
         then:
         result == module
 
         when:
-        include.realModulePath('xyz')
+        include.realModulePath('./xyz')
         then:
         thrown(NoSuchFileException)
 
@@ -98,21 +98,21 @@ class IncludeDefTest extends Specification {
         // when the module name reference a directory that contains
         // a file named 'main.nf', it's considered a module 'bundle'
         when:
-        def result = include.realModulePath('foo')
+        def result = include.realModulePath('./foo')
         then:
         result == module
 
         when:
-        include.realModulePath('bar')
+        include.realModulePath('./bar')
         then:
         thrown(NoSuchFileException)
 
         when:
         folder.resolve('bar').mkdir()
-        include.realModulePath('bar')
+        include.realModulePath('./bar')
         then:
         def e = thrown(ScriptCompilationException)
-        e.message == "Include 'bar' does not provide any module script -- the following path should contain a 'main.nf' script: '${folder.resolve('bar')}'"
+        e.message == "Include './bar' does not provide any module script -- the following path should contain a 'main.nf' script: '${folder.resolve('bar')}'"
     }
 
     def 'should check valid path' () {
@@ -137,6 +137,16 @@ class IncludeDefTest extends Specification {
         when:
         include.checkValidPath('this/dir')
         then:
+        noExceptionThrown()  // valid remote module reference (scope/name)
+
+        when:
+        include.checkValidPath('nf-core/fastqc')
+        then:
+        noExceptionThrown()  // valid remote module reference
+
+        when:
+        include.checkValidPath('invalid!')
+        then:
         thrown(IllegalModulePath)
 
         when:
diff --git a/modules/nf-lang/src/main/java/nextflow/script/control/ModuleResolver.java b/modules/nf-lang/src/main/java/nextflow/script/control/ModuleResolver.java
index f6e86d2878..c52931142a 100644
--- a/modules/nf-lang/src/main/java/nextflow/script/control/ModuleResolver.java
+++ b/modules/nf-lang/src/main/java/nextflow/script/control/ModuleResolver.java
@@ -76,9 +76,8 @@ private SourceUnit resolveInclude(IncludeNode node, SourceUnit sourceUnit, Funct
 
         var parent = Path.of(sourceUnit.getSource().getURI()).getParent();
 
-        // Resolve remote modules paths
-        if( source.startsWith("@") ) {
-            // Use SPI to get the remote module resolver implementation
+        // Resolve remote module paths (scope/name format, not starting with local prefixes)
+        if( isRemoteModule(source) ) {
             var modules = Path.of("./modules");
             var resolver = RemoteModuleResolverProvider.getInstance();
             resolver.resolve(source, modules.getParent());
@@ -98,6 +97,13 @@ private SourceUnit resolveInclude(IncludeNode node, SourceUnit sourceUnit, Funct
         return includeSource;
     }
 
+    static boolean isRemoteModule(String source) {
+        if( source.startsWith("/") || source.startsWith("./") || source.startsWith("../") )
+            return false;
+        // Must match scope/name pattern: scope is lowercase alphanumeric with dots/underscores/hyphens
+        return source.matches("^[a-z0-9][a-z0-9._\\-]*/[a-z][a-z0-9._\\-]*(/[a-z][a-z0-9._\\-]*)*$");
+    }
+
     private static URI getIncludeUri(Path parent, String source) {
         Path includePath = parent.resolve(source);
         if( Files.isDirectory(includePath) )
diff --git a/modules/nf-lang/src/main/java/nextflow/script/control/ResolveIncludeVisitor.java b/modules/nf-lang/src/main/java/nextflow/script/control/ResolveIncludeVisitor.java
index 04151fe4a7..b8bf711d93 100644
--- a/modules/nf-lang/src/main/java/nextflow/script/control/ResolveIncludeVisitor.java
+++ b/modules/nf-lang/src/main/java/nextflow/script/control/ResolveIncludeVisitor.java
@@ -22,7 +22,6 @@
 import java.util.List;
 import java.util.Set;
 
-import nextflow.module.spi.RemoteModuleResolverProvider;
 import nextflow.script.ast.FunctionNode;
 import nextflow.script.ast.IncludeNode;
 import nextflow.script.ast.ScriptNode;
@@ -85,7 +84,8 @@ public void visitInclude(IncludeNode node) {
             return;
         }
 
-        var parent = source.startsWith("@") ? Path.of("modules") : Path.of(uri).getParent();
+        var isRemoteModule = ModuleResolver.isRemoteModule(source);
+        var parent = isRemoteModule ? Path.of("modules") : Path.of(uri).getParent();
         var includeUri = getIncludeUri(parent, source);
         if( !isIncludeStale(node, includeUri) )
             return;