adjust for new plugin registry

Author: rpetit3

.gitignore

@@ -6,7 +6,3 @@
 # Ignore Gradle build output directory
 build
 work
-out
-
-# Bactopia related
-/bactopia/

.gitpod.yml

@@ -1,64 +1,21 @@
-config ?= compileClasspath
-
-ifdef module 
-mm = :${module}:
-else 
-mm = 
-endif 
+# Build the plugin
+assemble:
+	./gradlew assemble
 
 clean:
+	rm -rf .nextflow*
+	rm -rf work
+	rm -rf build
 	./gradlew clean
 
-compile:
-	./gradlew :nextflow:exportClasspath compileGroovy
-	@echo "DONE `date`"
-
-
-check:
-	./gradlew check
-
-
-#
-# Show dependencies try `make deps config=runtime`, `make deps config=google`
-#
-deps:
-	./gradlew -q ${mm}dependencies --configuration ${config}
-
-deps-all:
-	./gradlew -q dependencyInsight --configuration ${config} --dependency ${module}
-
-#
-# Refresh SNAPSHOTs dependencies
-#
-refresh:
-	./gradlew --refresh-dependencies 
-
-#
-# Run all tests or selected ones
-#
+# Run plugin unit tests
 test:
-ifndef class
-	./gradlew ${mm}test
-else
-	./gradlew ${mm}test --tests ${class}
-endif
-
-#
-# generate build zips under build/plugins
-# you can install the plugin copying manually these files to $HOME/.nextflow/plugins
-#
-buildPlugins:
-	./gradlew copyPluginZip
-
-#
-# Upload JAR artifacts to Maven Central
-#
-upload:
-	./gradlew upload
-
+	./gradlew test
 
-upload-plugins:
-	./gradlew plugins:upload
+# Install the plugin into local nextflow plugins dir
+install:
+	./gradlew install
 
-publish-index:
-	./gradlew plugins:publishIndex
+# Publish the plugin
+release:
+	./gradlew releasePlugin

.pre-commit-config.yaml

@@ -1,10 +1,11 @@
 # nf-bactopia
+
 A Nextflow plugin for specifically for usage with [Bactopia](https://bactopia.github.io/). It
 based of the modified [nf-core libs](https://github.com/bactopia/bactopia/tree/4b075af96da522222bb075d4b65927d1ba3de9c2/lib)
 and the [nf-schema plugin](https://github.com/nextflow-io/nf-schema).
 
 This plugin will replicate the functionality of the previous libraries, while being compatible
-with the Nextflow strict syntax (Nextflow version >= 24).
+with future releases of Nextflow (>= 25).
 
 Again, while you are free to do what you want, this plugin is specifically designed for Bactopia
 and will likely not work with other pipelines.
@@ -22,10 +23,22 @@ cd nf-bactopia
 ### Create a new conda environment
 
 ```{bash}
-conda create -n nf-bactopia \
+conda create -y -n nf-bactopia \
     -c conda-forge \
     -c bioconda \
-    gradle \
     make \
-    'nextflow>=24'
+    'nextflow>=25'
+conda activate nf-bactopia
+```
+
+### Build the plugin
+
+```{bash}
+make assemble
+```
+
+### Use the plugin
+
+```{bash}
+NXF_VER=25.06.0-edge NXF_PLUGINS_DIR=/path/to/build/plugins nextflow run ...
 ```

.prettierignore

@@ -0,0 +1,30 @@
+plugins {
+    id 'io.nextflow.nextflow-plugin' version '0.0.1-alpha4'
+}
+
+version = '0.1.0'
+
+dependencies {
+    // add here plugins dependencies
+    implementation 'org.json:json:20240303'
+    implementation 'dev.harrel:json-schema:1.5.0'
+    implementation 'com.sanctionco.jmail:jmail:1.6.3' // Needed for e-mail format validation
+}
+
+nextflowPlugin {
+    nextflowVersion = '24.10.0'
+
+    provider = 'bactopia'
+    className = 'bactopia.plugin.BactopiaPlugin'
+    extensionPoints = [
+        'bactopia.plugin.BactopiaExtension',
+        'bactopia.plugin.BactopiaFactory'
+    ]
+
+    publishing {
+        registry {
+            url = 'https://nf-plugins-registry.dev-tower.net/api'
+            authToken = project.findProperty('pluginRegistry.accessToken')
+        }
+    }
+}