Fix config options not being detected

CHANGELOG.md

@@ -1,3 +1,9 @@
+## 0.3.0
+
+1. Removed the hardcoded setup of samplesheet generation and migrated to a worksheet implementation to generate samplesheets. See the [worksheets](docs/worksheets.md) documentation for more information
+2. Use `clusters` to get the amount of reads for rnafusion runs instead of the `yield_`
+3. Resolved all configuration warnings
+
 ## 0.2.8
 
 1. Set the default mouse binsize to 100 if the given binsize is not 100 or 500

build.gradle

@@ -15,7 +15,8 @@ nextflowPlugin {
     className = 'nfcmgg.plugin.CmggPlugin'
     extensionPoints = [
         'nfcmgg.plugin.CmggExtension',
-        'nfcmgg.plugin.CmggFactory'
+        'nfcmgg.plugin.CmggFactory',
+        'nfcmgg.plugin.config.CmggConfig'
     ]
 
 }

src/main/groovy/nfcmgg/plugin/config/CmggConfig.groovy

@@ -32,13 +32,15 @@ import nextflow.script.dsl.Description
 @Description('The `cmgg` scope allows you to configure the nf-cmgg plugin.')
 class CmggConfig implements ConfigScope {
 
-    @ConfigOption
     @Description('Configuration scope for the creation of `DONE` files after successful pipeline execution.')
-    DoneConfig done
+    final DoneConfig done
 
-    @ConfigOption
     @Description('Configuration scope for the automatic generation of samplesheets for all supported pipelines.')
-    SamplesheetsConfig samplesheets
+    final SamplesheetsConfig samplesheets
+
+    // Keep the no-arg constructor in order to be able to use the `@ConfigOption` annotation
+    CmggConfig() {
+    }
 
     CmggConfig(Map config) {
         Map doneConfig = getMap(config?.done, 'cmgg.done')

src/main/groovy/nfcmgg/plugin/config/DoneConfig.groovy

@@ -34,11 +34,11 @@ class DoneConfig implements ConfigScope {
 
     @ConfigOption
     @Description('Create a DONE file after successful pipeline execution.')
-    Boolean enabled = false
+    final Boolean enabled = false
 
     @ConfigOption
     @Description('Location to create the DONE file after successful pipeline execution.')
-    Path location
+    final Path location
 
     DoneConfig(Map config) {
         this.enabled = getBoolean(config?.enabled, 'cmgg.done.enabled')

src/main/groovy/nfcmgg/plugin/config/SamplesheetsConfig.groovy

@@ -37,15 +37,15 @@ class SamplesheetsConfig implements ConfigScope {
 
     @ConfigOption
     @Description('Configuration scope for the creation of samplesheet files after successful pipeline execution.')
-    Boolean enabled = false
+    final Boolean enabled = false
 
     @ConfigOption
     @Description('Location to create the samplesheet files after successful pipeline execution.')
-    Path location
+    final Path location
 
     @ConfigOption
     @Description('A list of worksheets to use for the automatic samplesheet generation.')
-    List<Path> worksheets = []
+    final List<Path> worksheets = []
 
     SamplesheetsConfig(Map config) {
         this.enabled = getBoolean(config?.enabled, 'cmgg.samplesheets.enabled')