build: configure package manager plugins for proper compilation

- Update nf-conda and nf-pixi build.gradle to use standard Gradle plugins
- Add required MANIFEST.MF files with plugin metadata
- Register both plugins in settings.gradle
- Configure proper dependencies and source sets for plugin compilation

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <[email protected]>
Signed-off-by: Edmund Miller <[email protected]>

Author: edmundmiller

plugins/nf-conda/build.gradle

@@ -14,22 +14,32 @@
  * limitations under the License.
  */
 
-plugins {
-    id 'nextflow-plugin'
+apply plugin: 'java'
+apply plugin: 'java-test-fixtures'
+apply plugin: 'idea'
+apply plugin: 'groovy'
+
+sourceSets {
+    main.java.srcDirs = []
+    main.groovy.srcDirs = ['src/main']
+    main.resources.srcDirs = ['src/resources']
+    test.groovy.srcDirs = ['src/test']
+    test.java.srcDirs = []
+    test.resources.srcDirs = ['src/testResources']
 }
 
-group = 'io.nextflow'
-version = '1.0.0'
-gitBranch = 'main'
+configurations {
+    // see https://docs.gradle.org/4.1/userguide/dependency_management.html#sub:exclude_transitive_dependencies
+    runtimeClasspath.exclude group: 'org.slf4j', module: 'slf4j-api'
+}
 
 dependencies {
-    // plugin dependencies
-    api project(':nextflow')
+    compileOnly project(':nextflow')
+    compileOnly 'org.slf4j:slf4j-api:2.0.17'
+    compileOnly 'org.pf4j:pf4j:3.12.0'
 
-    // test dependencies
-    testImplementation(testFixtures(project(':nextflow')))
-    testImplementation 'org.codehaus.groovy:groovy-test:3.0.19'
-    testImplementation 'org.spockframework:spock-core:2.3-groovy-3.0'
-    testImplementation 'org.testcontainers:testcontainers:1.20.0'
-    testImplementation 'org.testcontainers:spock:1.20.0'
+    testImplementation(testFixtures(project(":nextflow")))
+    testImplementation project(':nextflow')
+    testImplementation "org.apache.groovy:groovy:4.0.28"
+    testImplementation "org.apache.groovy:groovy-nio:4.0.28"
 }

plugins/nf-conda/src/resources/META-INF/MANIFEST.MF

@@ -0,0 +1,6 @@
+Manifest-Version: 1.0
+Plugin-Class: nextflow.conda.CondaPlugin
+Plugin-Id: nf-conda
+Plugin-Version: 1.0.0
+Plugin-Provider: Seqera Labs
+Plugin-Requires: >=25.04.0

plugins/nf-pixi/build.gradle

@@ -14,22 +14,32 @@
  * limitations under the License.
  */
 
-plugins {
-    id 'nextflow-plugin'
+apply plugin: 'java'
+apply plugin: 'java-test-fixtures'
+apply plugin: 'idea'
+apply plugin: 'groovy'
+
+sourceSets {
+    main.java.srcDirs = []
+    main.groovy.srcDirs = ['src/main']
+    main.resources.srcDirs = ['src/resources']
+    test.groovy.srcDirs = ['src/test']
+    test.java.srcDirs = []
+    test.resources.srcDirs = ['src/testResources']
 }
 
-group = 'io.nextflow'
-version = '1.0.0'
-gitBranch = 'main'
+configurations {
+    // see https://docs.gradle.org/4.1/userguide/dependency_management.html#sub:exclude_transitive_dependencies
+    runtimeClasspath.exclude group: 'org.slf4j', module: 'slf4j-api'
+}
 
 dependencies {
-    // plugin dependencies
-    api project(':nextflow')
+    compileOnly project(':nextflow')
+    compileOnly 'org.slf4j:slf4j-api:2.0.17'
+    compileOnly 'org.pf4j:pf4j:3.12.0'
 
-    // test dependencies
-    testImplementation(testFixtures(project(':nextflow')))
-    testImplementation 'org.codehaus.groovy:groovy-test:3.0.19'
-    testImplementation 'org.spockframework:spock-core:2.3-groovy-3.0'
-    testImplementation 'org.testcontainers:testcontainers:1.20.0'
-    testImplementation 'org.testcontainers:spock:1.20.0'
+    testImplementation(testFixtures(project(":nextflow")))
+    testImplementation project(':nextflow')
+    testImplementation "org.apache.groovy:groovy:4.0.28"
+    testImplementation "org.apache.groovy:groovy-nio:4.0.28"
 }

plugins/nf-pixi/src/resources/META-INF/MANIFEST.MF

@@ -0,0 +1,6 @@
+Manifest-Version: 1.0
+Plugin-Class: nextflow.pixi.PixiPlugin
+Plugin-Id: nf-pixi
+Plugin-Version: 1.0.0
+Plugin-Provider: Seqera Labs
+Plugin-Requires: >=25.04.0

settings.gradle

@@ -43,3 +43,5 @@ include 'plugins:nf-codecommit'
 include 'plugins:nf-wave'
 include 'plugins:nf-cloudcache'
 include 'plugins:nf-k8s'
+include 'plugins:nf-conda'
+include 'plugins:nf-pixi'