Bump versions for 0.4.0 (#31)

* Perfect feel free to cut 0.7.0!

* 0.7.0

* bump the Nextflow Gradle plugin to

* add test dependency

* 0.7.0 -> 0.4.0

* 0.4.0

* beta.12

* Update CHANGELOG.md

update release date

* no need for this

Author: maxulysse

CHANGELOG.md

@@ -5,10 +5,11 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [Unreleased]
+## [0.4.0] - 2025-10-31
 
 ### Added
 
+- Updated Nextflow Gradle plugin from version 1.0.0-beta.9 to 1.0.0-beta.12 for improved plugin development support
 - New `getGenomeAttribute()` function to retrieve genome attributes from `params.genomes` for the selected genome
 
 ### Changed

build.gradle

@@ -1,11 +1,11 @@
 plugins {
-    id 'io.nextflow.nextflow-plugin' version '1.0.0-beta.9'
+    id 'io.nextflow.nextflow-plugin' version '1.0.0-beta.12'
 }
 
-version = '0.3.1'
+version = '0.4.0'
 
 nextflowPlugin {
-    nextflowVersion = '25.04.0'
+    nextflowVersion = '25.10.0'
 
     provider = 'nf-core'
     className = 'nfcore.plugin.NfUtilsPlugin'

validation/README.md

@@ -34,7 +34,7 @@ Demonstrates the migration from local pipeline utility functions to plugin-based
 
 ```bash
 # Run individual test
-nextflow run validation/version-topic-channels/ -plugins nf-core-utils@0.3.0
+nextflow run validation/version-topic-channels/ -plugins nf-core-utils@0.4.0
 
 # Or use the old validation script
 ./validation/validate.sh
@@ -109,13 +109,13 @@ Run tests directly with Nextflow:
 
 ```bash
 # Individual test execution
-nextflow run validation/version-topic-channels/ -plugins nf-core-utils@0.3.0
-nextflow run validation/config-validation/ -plugins nf-core-utils@0.3.0
-nextflow run validation/notification-system/ -plugins nf-core-utils@0.3.0
-nextflow run validation/pipeline-utilities/ -plugins nf-core-utils@0.3.0
+nextflow run validation/version-topic-channels/ -plugins nf-core-utils@0.4.0
+nextflow run validation/config-validation/ -plugins nf-core-utils@0.4.0
+nextflow run validation/notification-system/ -plugins nf-core-utils@0.4.0
+nextflow run validation/pipeline-utilities/ -plugins nf-core-utils@0.4.0
 
 # With different profiles
-nextflow run validation/version-topic-channels/ -plugins nf-core-utils@0.3.0 -profile test
+nextflow run validation/version-topic-channels/ -plugins nf-core-utils@0.4.0 -profile test
 ```
 
 ### Quick Validation (All Tests)

validation/config-validation/README.md

@@ -101,15 +101,15 @@ if (!checkCondaChannels()) {
 
 ```bash
 # Basic validation
-nextflow run validation/config-validation/ -plugins nf-core-utils@0.3.0
+nextflow run validation/config-validation/ -plugins nf-core-utils@0.4.0
 
 # With different profiles to test profile validation
-nextflow run validation/config-validation/ -plugins nf-core-utils@0.3.0 -profile test
-nextflow run validation/config-validation/ -plugins nf-core-utils@0.3.0 -profile docker
-nextflow run validation/config-validation/ -plugins nf-core-utils@0.3.0 -profile test,conda
+nextflow run validation/config-validation/ -plugins nf-core-utils@0.4.0 -profile test
+nextflow run validation/config-validation/ -plugins nf-core-utils@0.4.0 -profile docker
+nextflow run validation/config-validation/ -plugins nf-core-utils@0.4.0 -profile test,conda
 
 # With debug logging
-nextflow run validation/config-validation/ -plugins nf-core-utils@0.3.0 -profile debug
+nextflow run validation/config-validation/ -plugins nf-core-utils@0.4.0 -profile debug
 ```
 
 ### Via Validation Suite
@@ -119,7 +119,7 @@ nextflow run validation/config-validation/ -plugins [email protected] -profile
 ./validation/validate-all.sh
 
 # Run just configuration validation
-nextflow run validation/config-validation/ -plugins nf-core-utils@0.3.0
+nextflow run validation/config-validation/ -plugins nf-core-utils@0.4.0
 ```
 
 ## Expected Outputs

validation/nextflow.config

@@ -1,5 +1,5 @@
 plugins {
-    id 'nf-core-utils@0.3.1'
+    id 'nf-core-utils@0.4.0'
 }
 
 // Basic configuration for integration tests

validation/nf-test.config

@@ -9,7 +9,7 @@ config {
     autoSort false
 
     // Global Nextflow options for validation tests
-    options "-plugins nf-core-utils@0.3.1 --validate_params false"
+    options "-plugins nf-core-utils@0.4.0 --validate_params false"
 
     // Include plugins
     plugins {

validation/pipeline-utilities/README.md

@@ -72,13 +72,13 @@ dumpParametersToJSON(params.outdir, params)
 
 ```bash
 # Basic validation
-nextflow run validation/pipeline-utilities/ -plugins nf-core-utils@0.3.0
+nextflow run validation/pipeline-utilities/ -plugins nf-core-utils@0.4.0
 
 # With test profile (faster)
-nextflow run validation/pipeline-utilities/ -plugins nf-core-utils@0.3.0 -profile test
+nextflow run validation/pipeline-utilities/ -plugins nf-core-utils@0.4.0 -profile test
 
 # With debug logging
-nextflow run validation/pipeline-utilities/ -plugins nf-core-utils@0.3.0 -profile debug
+nextflow run validation/pipeline-utilities/ -plugins nf-core-utils@0.4.0 -profile debug
 ```
 
 ### Via Validation Suite

validation/topic-channel-citations/README.md

@@ -104,10 +104,10 @@ make install
 
 # Run validation test
 cd validation/topic-channel-citations
-nextflow run . -plugins nf-core-utils@0.3.0
+nextflow run . -plugins nf-core-utils@0.4.0
 
 # Test with optional tool enabled
-nextflow run . -plugins nf-core-utils@0.3.0 --run_optional true
+nextflow run . -plugins nf-core-utils@0.4.0 --run_optional true
 ```
 
 ## Expected Output

validation/topic-channel-citations/nextflow.config

@@ -8,7 +8,7 @@ params {
 
 // Plugin configuration
 plugins {
-    id 'nf-core-utils@0.3.0'
+    id 'nf-core-utils@0.4.0'
 }
 
 manifest {

validation/version-topic-channels/README.md

@@ -53,13 +53,13 @@ ch_versions
 
 ```bash
 # Basic validation
-nextflow run validation/ -plugins nf-core-utils@0.3.0
+nextflow run validation/ -plugins nf-core-utils@0.4.0
 
 # With test profile (faster)
-nextflow run validation/ -plugins nf-core-utils@0.3.0 -profile test
+nextflow run validation/ -plugins nf-core-utils@0.4.0 -profile test
 
 # With debug logging
-nextflow run validation/ -plugins nf-core-utils@0.3.0 -profile debug
+nextflow run validation/ -plugins nf-core-utils@0.4.0 -profile debug
 ```
 
 ### Expected Output