Fix meta.yaml -> meta.yml, module manifest -> module spec

Signed-off-by: Ben Sherman <bentshermann@gmail.com>

Author: bentsherman

adr/20251114-module-system.md

@@ -11,13 +11,13 @@
 ### Version 2.7 (2026-03-09)
 - **Renamed `.checksum` to `.module-info`**: Leaves room for additional properties in the future
 - **Removed `@` prefix from module scopes**: Local modules are distinguished from remote modules by presence/absence of `./` prefix
-- **Removed version pinning from config**: Installed module versions are now inferred from the `meta.yaml` of each module in the `modules/` directory instead of being declared in `nextflow.config`
+- **Removed version pinning from config**: Installed module versions are now inferred from the `meta.yml` of each module in the `modules/` directory instead of being declared in `nextflow.config`
 
 ### Version 2.6 (2026-01-28)
 - **Removed module parameters**: Module parameters specification moved to separate spec document.
 
 ### Version 2.5 (2026-01-23)
-- **Module parameters**: Replaced structured tool arguments with general module parameters defined in `meta.yaml`
+- **Module parameters**: Replaced structured tool arguments with general module parameters defined in `meta.yml`
 - **Simplified tools section**: Removed `args` property from tools; tool arguments now configured via module parameters
 - **Simplified `requires` block**: Removed `plugins`, `modules`, and `subworkflows` sub-properties; `requires` now only contains `nextflow` version constraint
 - **Process modules focus**: Removed sub-workflow references; spec is now focused on process modules only
@@ -74,7 +74,7 @@ include { MY_PROCESS } from './modules/my-process.nf'
 
 **Module Naming**: Scoped modules `scope/name` (e.g., `nf-core/salmon`, `myorg/custom`). Local paths supported for backwards compatibility. No nested paths with the module are allowed - each module must have a `main.nf` as the entry point.
 
-**Version Resolution**: Installed module versions are inferred from the `meta.yaml` of each module in the `modules/` directory. If a module is not present locally, the latest available version is downloaded from the registry.
+**Version Resolution**: Installed module versions are inferred from the `meta.yml` of each module in the `modules/` directory. If a module is not present locally, the latest available version is downloaded from the registry.
 
 **Resolution Order**:
 1. Check local `modules/scope/name/` exists
@@ -86,7 +86,7 @@ include { MY_PROCESS } from './modules/my-process.nf'
 | Local State | Action |
 |-------------|--------|
 | Missing | Download latest from registry |
-| Exists, checksum valid | Use local module (version from `meta.yaml`) |
+| Exists, checksum valid | Use local module (version from `meta.yml`) |
 | Exists, checksum mismatch | **Warn**: locally modified, will NOT replace unless `-force` is used |
 
 **Key Behaviors**:
@@ -120,7 +120,7 @@ registry {
 }
 ```
 
-**Module Spec** (`meta.yaml`):
+**Module Spec** (`meta.yml`):
 ```yaml
 name: nf-core/bwa-align
 version: 1.2.4                    # This module's version
@@ -158,7 +158,7 @@ This avoids introducing new notation that would require additional parser suppor
 
 **Module Resolution**:
 
-Installed module versions are inferred from the `meta.yaml` file for each module in the `modules/` directory.
+Installed module versions are inferred from the `meta.yml` file for each module in the `modules/` directory.
 
 ### 3. Unified Nextflow Registry
 
@@ -190,7 +190,7 @@ Note: The `{name}` parameter includes the namespace prefix (e.g., "nf-core/fastq
 
 **Artifact Types**:
 - **Plugins**: JAR files with JSON metadata, resolved at startup
-- **Modules**: Source archives (.nf + meta.yaml), resolved at parse time
+- **Modules**: Source archives (.nf + meta.yml), resolved at parse time
 
 **Benefits**:
 - Reuses existing infrastructure (HTTP service, S3 storage, authentication)
@@ -318,7 +318,7 @@ Display the status of all modules, comparing what is configured in `nextflow.con
 
 **Output columns**:
 - Module name (`scope/name`)
-- Installed version (from `modules/scope/name/meta.yaml`)
+- Installed version (from `modules/scope/name/meta.yml`)
 - Latest available version (from registry)
 - Status indicator (up-to-date, outdated, missing)
 
@@ -364,15 +364,15 @@ Publish a module to the Nextflow registry, making it available for others to ins
 - `-dry-run`: Validate without publishing
 
 **Behavior**:
-1. Validates `meta.yaml` schema and required fields (name, version, description)
+1. Validates `meta.yml` schema and required fields (name, version, description)
 2. Verifies that `main.nf` exists and is valid Nextflow syntax
 3. Verifies that `README.md` documentation is present
 4. Authenticates with registry using configured credentials
 5. Creates a release draft and uploads the module archive
 6. Publishes the release, making it available for installation
 
 **Requirements**:
-- Valid `meta.yaml` with name, version, and description
+- Valid `meta.yml` with name, version, and description
 - `main.nf` entry point file
 - `README.md` documentation
 - Authentication token configured in `registry.auth` or `NXF_REGISTRY_TOKEN`
@@ -391,12 +391,12 @@ Everything within the module directory should be uploaded. Module bundle should
 ```
 my-module/
 ├── main.nf      # Required: entry point for module
-├── meta.yaml    # Required: Module spec (version, metadata, I/O specs)
+├── meta.yml    # Required: Module spec (version, metadata, I/O specs)
 ├── README.md    # Required: Module description
 └── tests/       # Optional tests
 ```
 
-**Module Spec extension** (`meta.yaml`):
+**Module Spec extension** (`meta.yml`):
 ```yaml
 name: nf-core/bwa-align
 version: 1.2.4              # This module's version
@@ -418,16 +418,16 @@ project-root/
     ├── nf-core/
     │   ├── bwa-align/
     │   │   ├── .module-info        # Cached registry checksum
-    │   │   ├── meta.yaml
+    │   │   ├── meta.yml
     │   │   └── main.nf             # Required entry point
     │   └── samtools/view/
     │       ├── .module-info
-    │       ├── meta.yaml
+    │       ├── meta.yml
     │       └── main.nf             # Required entry point
     └── myorg/
         └── custom-process/
             ├── .module-info
-            ├── meta.yaml
+            ├── meta.yml
             └── main.nf             # Required entry point
 ```
 
@@ -455,12 +455,12 @@ project-root/
 1. Parse `include` statements → extract module names (e.g., `nf-core/bwa-align`)
 2. For each module:
    a. Check local `modules/scope/name/` exists
-      - If exists → read installed version from `modules/scope/name/meta.yaml`
+      - If exists → read installed version from `modules/scope/name/meta.yml`
       - If missing → download latest version from registry
    b. Verify local module integrity against `.module-info` file
       - Checksum mismatch → warn and do NOT override (local changes detected)
 3. On download: store module to `modules/scope/name/` with `.module-info` file
-4. Read `meta.yaml` file: Validates Nextflow requirement → Fail if not fulfilled
+4. Read `meta.yml` file: Validates Nextflow requirement → Fail if not fulfilled
 5. Parse module's `main.nf` file → make processes available
 
 **Security**:
@@ -484,7 +484,7 @@ project-root/
 | Metadata | JSON spec | YAML spec |
 | Naming | `nf-amazon` | `nf-core/salmon` |
 | Cache Location | `$NXF_HOME/plugins/` | `modules/scope/name/` |
-| Version Config | `plugins {}` in config | `meta.yaml` in `modules/` directory |
+| Version Config | `plugins {}` in config | `meta.yml` in `modules/` directory |
 | Registry Path | `/api/v1/plugins/` | `/api/modules/{name}` |
 
 ## Rationale
@@ -495,9 +495,9 @@ project-root/
 - Lower operational overhead
 - Type-specific handling maintains separation of concerns
 
-**Why infer versions from `meta.yaml` instead of pinning in a separate file?**
+**Why infer versions from `meta.yml` instead of pinning in a separate file?**
 - Simple: install a version once and it is captured in the module files
-- Reproducibility via committing the `modules/` directory (including `meta.yaml`) to the project git repository
+- Reproducibility via committing the `modules/` directory (including `meta.yml`) to the project git repository
 - Reduces configuration burden: no need to keep config in sync with installed state
 
 **Why parse-time resolution?**
@@ -520,12 +520,12 @@ project-root/
 
 **Positive**:
 - Enables ecosystem-wide code reuse
-- Reproducible workflows via committing the `modules/` directory (including `meta.yaml`) to the project git repository
+- Reproducible workflows via committing the `modules/` directory (including `meta.yml`) to the project git repository
 - Centralized discovery and distribution via unified registry
 - Minimal operational overhead (single registry for both plugins and modules)
 - Module scoping enables organization namespaces and private registries
 - Local `modules/` directory provides project isolation
-- No version duplication: installed `meta.yaml` is the single source of truth
+- No version duplication: installed `meta.yml` is the single source of truth
 - Simple module structure: each module has single `main.nf` entry point
 
 **Negative**:
@@ -548,7 +548,7 @@ project-root/
 
 ## Appendix A: Module Schema Specification
 
-This appendix defines the JSON schema for module `meta.yaml` files. The schema maintains backward compatibility with existing nf-core module metadata patterns while supporting the new Nextflow module system features.
+This appendix defines the JSON schema for module `meta.yml` files. The schema maintains backward compatibility with existing nf-core module metadata patterns while supporting the new Nextflow module system features.
 
 **Schema File:** [module-spec-schema.json](module-spec-schema.json)
 **Published URL:** `https://registry.nextflow.io/schemas/module-spec/v1.0.0`
@@ -761,7 +761,7 @@ output:
 
 #### Schema Validation
 
-Use the schema reference in your `meta.yaml`:
+Use the schema reference in your `meta.yml`:
 
 ```yaml
 # yaml-language-server: $schema=https://registry.nextflow.io/schemas/module-spec/v1.0.0

adr/module-spec-schema.json

@@ -2,12 +2,12 @@
   "$schema": "https://json-schema.org/draft/2020-12/schema",
   "$id": "https://raw.githubusercontent.com/nextflow-io/schemas/main/module/v1/schema.json",
   "title": "Nextflow Module Schema",
-  "description": "Schema for Nextflow module meta.yaml files, supporting both nf-core community patterns and the Nextflow module system",
+  "description": "Schema for Nextflow module meta.yml files, supporting both nf-core community patterns and the Nextflow module system",
   "type": "object",
   "properties": {
     "name": {
       "type": "string",
-      "description": "Module name. Can be a simple identifier (e.g., 'fastqc', 'bwa_mem') for local/nf-core modules, or a fully qualified scoped name (e.g., 'nf-core/fastqc', 'myorg/custom') for registry modules. Note: The '@' prefix is only used in DSL include statements, not in meta.yaml",
+      "description": "Module name. Can be a simple identifier (e.g., 'fastqc', 'bwa_mem') for local/nf-core modules, or a fully qualified scoped name (e.g., 'nf-core/fastqc', 'myorg/custom') for registry modules.",
       "examples": ["fastqc", "bwa_mem", "nf-core/fastqc", "myorg/salmon-quant"],
       "pattern": "^([a-z0-9][a-z0-9-]*/)?[a-z][a-z0-9_-]*$"
     },

docs/cli.md

@@ -386,7 +386,7 @@ $ nextflow module publish myorg/my-module
 $ nextflow module publish myorg/my-module -dry-run
 ```
 
-Publishing requires authentication via the `NXF_REGISTRY_TOKEN` environment variable or `registry.apiKey` in the Nextflow configuration. The module must include `main.nf`, `meta.yaml`, and `README.md` files.
+Publishing requires authentication via the `NXF_REGISTRY_TOKEN` environment variable or `registry.apiKey` in the Nextflow configuration. The module must include `main.nf`, `meta.yml`, and `README.md` files.
 
 Use `-dry-run` to validate your module structure without uploading.
 

docs/module.md

@@ -389,7 +389,7 @@ The argument can be either a `scope/name` reference (for an already-installed mo
 Your module directory must include:
 
 - `main.nf`: The module entry point
-- `meta.yaml`: Module metadata (name, description, version, etc.)
+- `meta.yml`: Module spec (name, description, version, etc.)
 - `README.md`: Module documentation
 
 Authentication is required for publishing and can be provided via the `NXF_REGISTRY_TOKEN` environment variable or in your configuration:
@@ -432,8 +432,8 @@ modules/
     └── module-name/
         ├── .module-info     # Integrity checksum (generated automatically)
         ├── README.md        # Documentation (required for publishing)
-        ├── main.nf          # Module entry point (required)
-        ├── meta.yaml        # Module metadata (required for publishing)
+        ├── main.nf          # Module script (required)
+        ├── meta.yml         # Module spec (required for publishing)
         ├── resources/       # Optional: module binaries and resources
         └── templates/       # Optional: process templates
 ```

docs/reference/cli.md

@@ -1308,7 +1308,7 @@ The `module` command provides a comprehensive system for managing reusable, regi
 : Publish a module to the registry, making it available for others to install.
 : The argument can be either a `scope/name` reference (for an already-installed module) or a local directory path containing the module files.
 : Requires authentication via `NXF_REGISTRY_TOKEN` environment variable or `registry.apiKey` configuration.
-: The module directory must contain `main.nf`, `meta.yaml`, and `README.md`.
+: The module directory must contain `main.nf`, `meta.yml`, and `README.md`.
 : The following options are available:
 
   `-dry-run`

modules/nextflow/src/main/groovy/nextflow/cli/module/CmdModulePublish.groovy

@@ -88,21 +88,21 @@ class CmdModulePublish extends CmdBase {
             )
         }
 
-        // Step 2: Load and validate manifest
+        // Step 2: Load and validate spec
         def manifestPath = moduleDir.resolve(ModuleStorage.MODULE_MANIFEST_FILE)
-        def manifest = ModuleSpec.load(manifestPath)
+        def spec = ModuleSpec.load(manifestPath)
 
-        def manifestErrors = manifest.validate()
+        def manifestErrors = spec.validate()
         if (!manifestErrors.isEmpty()) {
             throw new AbortOperationException(
-                "Module manifest validation failed:\n" + manifestErrors.collect { "  - ${it}" }.join('\n')
+                "Module spec validation failed:\n" + manifestErrors.collect { "  - ${it}" }.join('\n')
             )
         }
 
-        log.info "Module validated: ${manifest.name}@${manifest.version}"
+        log.info "Module validated: ${spec.name}@${spec.version}"
 
         if (dryRun) {
-            printDryRunInfo(manifest)
+            printDryRunInfo(spec)
             return
         }
 
@@ -114,11 +114,11 @@ class CmdModulePublish extends CmdBase {
 
         def registryConfig = config.navigate('registry') as RegistryConfig ?: new RegistryConfig()
 
-        publishModule(moduleDir, registryConfig, manifest)
+        publishModule(moduleDir, registryConfig, spec)
 
     }
 
-    private void publishModule(Path moduleDir, RegistryConfig registryConfig, ModuleSpec manifest){
+    private void publishModule(Path moduleDir, RegistryConfig registryConfig, ModuleSpec spec){
         log.info "Creating module bundle..."
         def tempBundleFile = Files.createTempFile("nf-module-publish-", ".tar.gz")
 
@@ -131,15 +131,15 @@ class CmdModulePublish extends CmdBase {
 
             // Create publish request as a map (npr-api will serialize it)
             def request = [
-                version: manifest.version,
+                version: spec.version,
                 bundle: bundleBytes
             ]
 
             // Publish to registry
             final registry = registryUrl ?: registryConfig.url
             log.info "Publishing module to registry: ${registryUrl ?: registryConfig.url}"
             def registryClient = new ModuleRegistryClient(registryConfig)
-            def response = registryClient.publishModule(manifest.name, request, registry)
+            def response = registryClient.publishModule(spec.name, request, registry)
 
             if (useModuleReference) {
                 // If publish is performed using the module reference we should create/update the .module-info with the correct checksum
@@ -152,13 +152,13 @@ class CmdModulePublish extends CmdBase {
             println "✓ Module published successfully!"
             println ""
             println "Module details:"
-            println "  Name: ${manifest.name}"
-            println "  Version: ${manifest.version}"
+            println "  Name: ${spec.name}"
+            println "  Version: ${spec.version}"
             println "  DownloadUrl: ${response.downloadUrl}"
 
             println ""
             println "Others can now install this module using:"
-            println "  nextflow module install ${manifest.name}"
+            println "  nextflow module install ${spec.name}"
 
         } finally {
             // Clean up temporary bundle file
@@ -172,23 +172,23 @@ class CmdModulePublish extends CmdBase {
         }
     }
 
-    private void printDryRunInfo(ModuleSpec manifest) {
+    private void printDryRunInfo(ModuleSpec spec) {
         println "✓ Module structure is valid"
         println ""
         println "Module details:"
-        println "  Name: ${manifest.name}"
-        println "  Version: ${manifest.version}"
-        println "  Description: ${manifest.description}"
-        println "  License: ${manifest.license}"
-        if( manifest.authors ) {
-            println "  Authors: ${manifest.authors.join(', ')}"
+        println "  Name: ${spec.name}"
+        println "  Version: ${spec.version}"
+        println "  Description: ${spec.description}"
+        println "  License: ${spec.license}"
+        if( spec.authors ) {
+            println "  Authors: ${spec.authors.join(', ')}"
         }
-        if( manifest.keywords ) {
-            println "  Keywords: ${manifest.keywords.join(', ')}"
+        if( spec.keywords ) {
+            println "  Keywords: ${spec.keywords.join(', ')}"
         }
-        if( manifest.requires ) {
+        if( spec.requires ) {
             println "  Requires:"
-            manifest.requires.each { name, version ->
+            spec.requires.each { name, version ->
                 println "    - ${name}: ${version}"
             }
         }