nextflow-io · bentsherman · Mar 6, 2026 · Mar 6, 2026 · Mar 6, 2026 · Mar 6, 2026
diff --git 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
@@ -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
@@ -111,15 +111,15 @@ 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 ""
     }
 
     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
@@ -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
@@ -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
@@ -105,17 +103,17 @@ 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)"
             }
 
             // 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
@@ -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
@@ -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)
     }
-}
+}
diff --git 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
@@ -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
@@ -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}"
     }
 
     /**
@@ -65,23 +65,14 @@ 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"
             )
         }
 
         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