Restore final qualifiers and tidy whitespace in file scopes

- Mark file/enabled/overwrite/maxTasks final on the four nested file scopes
  and final on name/ending/defaultEnabled in BaseFileConfig (each is
  assigned exactly once in a constructor body)
- Normalise whitespace: drop trailing spaces and double-space after `=`
- Add CHANGELOG entry under New > Bug Fixes

Signed-off-by: Jonathan Manning <jonathan.manning@seqera.io>

Author: pinin4fjords

CHANGELOG.md

@@ -1,5 +1,6 @@
 # New
 ## Bug Fixes:
+- Eliminated `Unrecognized config option` warnings under Nextflow's v2 syntax parser by registering `CO2FootprintConfig` as an extension point and aligning the nested file-config scopes with the v2 `ConfigScope` discovery rules
 
 ## Misc:
 

src/main/nextflow/co2footprint/Config/BaseFileConfig.groovy

@@ -13,12 +13,13 @@ import java.nio.file.Path
  */
 @Slf4j
 class BaseFileConfig {
-    String name
-    String ending
-    boolean defaultEnabled
+    final String name
+    final String ending
+    final boolean defaultEnabled
 
     protected final LinkedHashSet<String> usedKeys = [] as LinkedHashSet<String>
-    
+
+
     /**
      * Parses a file-based sub-configuration for nf-co2footprint and sets up defaults and fallbacks.
      *
@@ -33,7 +34,7 @@ class BaseFileConfig {
 
     /**
      * Define a file path from the given config map and timestamp, as well as predefined variables.
-     * 
+     *
      * @param fileConfig The general config of this file.
      * @param timestamp A timestamp string.
      * @return The path to the file.

src/main/nextflow/co2footprint/Config/ProvenanceFileConfig.groovy

@@ -12,15 +12,15 @@ class ProvenanceFileConfig extends BaseFileConfig implements ConfigScope {
 
     @ConfigOption
     @Description('Path to the file.')
-    Path file
+    final Path file
 
     @ConfigOption
     @Description('Whether to enable the file creation.')
-    Boolean enabled
+    final Boolean enabled
 
     @ConfigOption
     @Description('Whether to overwrite a file if it already exists.')
-    Boolean overwrite
+    final Boolean overwrite
 
     @ConfigOption
     @Description('Whether only emission metrics should be reported in the provenance file.')
@@ -30,7 +30,7 @@ class ProvenanceFileConfig extends BaseFileConfig implements ConfigScope {
         super('provenance', 'json', false)
 
         file = defineFile(provenanceFileConfig, timestamp)
-        enabled =  defineEnabled(provenanceFileConfig)
+        enabled = defineEnabled(provenanceFileConfig)
         overwrite = defineOverwrite(provenanceFileConfig)
 
         emissionMetricsOnly = provenanceFileConfig.containsKey('emissionMetricsOnly') ?

src/main/nextflow/co2footprint/Config/ReportFileConfig.groovy

@@ -12,27 +12,27 @@ class ReportFileConfig extends BaseFileConfig implements ConfigScope {
 
     @ConfigOption
     @Description('Path to the file.')
-    Path file
+    final Path file
 
     @ConfigOption
     @Description('Whether to enable the file creation.')
-    Boolean enabled
+    final Boolean enabled
 
     @ConfigOption
     @Description('Whether to overwrite a file if it already exists.')
-    Boolean overwrite
+    final Boolean overwrite
 
     @ConfigOption
     @Description('The number of maximum tasks that is displayed in the report.')
-    Integer maxTasks
+    final Integer maxTasks
 
     ReportFileConfig(Map reportFileConfig, String timestamp=null) {
         super('report', 'html')
 
         file = defineFile(reportFileConfig, timestamp)
-        enabled =  defineEnabled(reportFileConfig)
+        enabled = defineEnabled(reportFileConfig)
         overwrite = defineOverwrite(reportFileConfig)
-        
+
         maxTasks = reportFileConfig.containsKey('maxTasks') ?
                 CO2FootprintConfig.getCollect('maxTasks', reportFileConfig, usedKeys) as Integer :
                 10_000

src/main/nextflow/co2footprint/Config/SummaryFileConfig.groovy

@@ -8,27 +8,27 @@ import nextflow.script.dsl.Description
 import java.nio.file.Path
 
 @Description('The `co2footprint.summary` scope allows you to configure the summary file of the `nf-co2footprint` plugin.')
-class SummaryFileConfig extends BaseFileConfig implements ConfigScope{
+class SummaryFileConfig extends BaseFileConfig implements ConfigScope {
 
     @ConfigOption
     @Description('Path to the file.')
-    Path file
+    final Path file
 
     @ConfigOption
     @Description('Whether to enable the file creation.')
-    Boolean enabled
+    final Boolean enabled
 
     @ConfigOption
     @Description('Whether to overwrite a file if it already exists.')
-    Boolean overwrite
+    final Boolean overwrite
 
     SummaryFileConfig(Map summaryFileConfig, String timestamp=null) {
         super('summary', 'txt')
 
         file = defineFile(summaryFileConfig, timestamp)
-        enabled =  defineEnabled(summaryFileConfig)
+        enabled = defineEnabled(summaryFileConfig)
         overwrite = defineOverwrite(summaryFileConfig)
-        
+
         CO2FootprintConfig.checkKeyUsage(summaryFileConfig, usedKeys)
     }
 }

src/main/nextflow/co2footprint/Config/TraceFileConfig.groovy

@@ -8,25 +8,25 @@ import nextflow.script.dsl.Description
 import java.nio.file.Path
 
 @Description('The `co2footprint.trace` scope allows you to configure the trace file of the `nf-co2footprint` plugin.')
-class TraceFileConfig extends BaseFileConfig implements ConfigScope{
+class TraceFileConfig extends BaseFileConfig implements ConfigScope {
 
     @ConfigOption
     @Description('Path to the file.')
-    Path file
+    final Path file
 
     @ConfigOption
     @Description('Whether to enable the file creation.')
-    Boolean enabled
+    final Boolean enabled
 
     @ConfigOption
     @Description('Whether to overwrite a file if it already exists.')
-    Boolean overwrite
-    
+    final Boolean overwrite
+
     TraceFileConfig(Map traceFileConfig, String timestamp=null) {
         super('trace', 'txt')
-        
+
         file = defineFile(traceFileConfig, timestamp)
-        enabled =  defineEnabled(traceFileConfig)
+        enabled = defineEnabled(traceFileConfig)
         overwrite = defineOverwrite(traceFileConfig)
 
         CO2FootprintConfig.checkKeyUsage(traceFileConfig, usedKeys)