minor edits

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

Author: bentsherman

docs/module.md

@@ -362,8 +362,8 @@ $ nextflow module remove nf-core/fastqc
 
 By default, both the module files and the `.module-info` file are removed. Use the flags below to control this behaviour:
 
-- `-keep-files` — Remove the `.module-info` file created at install but keep the rest of files
-- `-force` — Force removal even if the module has no `.module-info` file (i.e. not installed from a registry) or has local modifications
+- `-keep-files`: Remove the `.module-info` file created at install but keep the rest of files
+- `-force`: Force removal even if the module has no `.module-info` file (i.e. not installed from a registry) or has local modifications
 
 ### Viewing module information
 
@@ -430,7 +430,7 @@ Registry modules follow a standard directory structure:
 modules/
 └── scope/
     └── module-name/
-        ├── .checksum        # Integrity checksum (generated automatically)
+        ├── .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)

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

@@ -65,10 +65,7 @@ class DefaultRemoteModuleResolver implements RemoteModuleResolver {
             log.debug "Module ${reference} resolved to ${mainFile}"
             return mainFile
         } catch (Exception e) {
-            throw new IllegalModulePath(
-                "Failed to resolve remote module ${moduleName}: ${e.message}",
-                e
-            )
+            throw new IllegalModulePath("Failed to resolve remote module ${moduleName}: ${e.message}", e)
         }
     }
 

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

@@ -31,7 +31,7 @@ import java.util.regex.Pattern
 @EqualsAndHashCode
 class ModuleReference {
 
-    // Pattern allows: optional @, scope with letters/digits/hyphens/dots/underscores, name segments separated by slashes (no trailing slash)
+    // Pattern allows: 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._\-]*)*)$/
@@ -47,7 +47,7 @@ class ModuleReference {
     }
 
     /**
-     * Parse a module reference from a string in "@scope/name" or "scope/name" format
+     * Parse a module reference from a string as "scope/name"
      *
      * @param source The module reference string
      * @return A ModuleReference object

modules/nextflow/src/main/resources/META-INF/extensions.idx

@@ -18,8 +18,8 @@ nextflow.cache.DefaultCacheFactory
 nextflow.conda.CondaConfig
 nextflow.config.ConfigMap
 nextflow.config.Manifest
-nextflow.config.WorkflowConfig
 nextflow.config.RegistryConfig
+nextflow.config.WorkflowConfig
 nextflow.container.ApptainerConfig
 nextflow.container.CharliecloudConfig
 nextflow.container.DockerConfig

modules/nextflow/src/testFixtures/groovy/test/TestHelper.groovy

@@ -16,17 +16,16 @@
 
 package test
 
-import com.google.common.jimfs.JimfsPath
-import nextflow.util.KryoHelper
-import nextflow.util.PathSerializer
-
 import java.nio.file.Files
 import java.nio.file.Path
 import java.util.zip.GZIPInputStream
 
 import com.google.common.jimfs.Configuration
 import com.google.common.jimfs.Jimfs
+import com.google.common.jimfs.JimfsPath
 import groovy.transform.Memoized
+import nextflow.util.KryoHelper
+import nextflow.util.PathSerializer
 /**
  *
  * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>

modules/nf-commons/src/main/nextflow/config/RegistryConfig.groovy

@@ -36,15 +36,15 @@ import nextflow.script.dsl.Description
 @CompileStatic
 class RegistryConfig implements ConfigScope {
 
-    final static public String DEFAULT_REGISTRY_URL = 'https://registry.nextflow.io/api'
+    public static final String DEFAULT_REGISTRY_URL = 'https://registry.nextflow.io/api'
 
     @ConfigOption
     @Description("Registry URL or list of registry URLs in priority order (primary URL first)")
-    final private Collection<String> url
+    private final Collection<String> url
 
     @ConfigOption
     @Description("API key for authenticating with the primary registry")
-    final private String apiKey
+    private final String apiKey
 
     /* required by extension point -- do not remove */
     RegistryConfig() {

settings.gradle

@@ -49,5 +49,5 @@ include 'plugins:nf-cloudcache'
 include 'plugins:nf-k8s'
 include 'plugins:nf-seqera'
 
-//includeBuild '../sched'
 //includeBuild('../plugin-registry')
+//includeBuild '../sched'