add nextflow d30e48d

2026-04-29 23:01:54 +02:00
parent d0b12d668d
commit 97cc9058d3
2840 changed files with 730250 additions and 0 deletions
--- a/nextflow/plugins/nf-wave/build.gradle
+++ b/nextflow/plugins/nf-wave/build.gradle
@@ -0,0 +1,71 @@
+/*
+ * Copyright 2013-2026, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+plugins {
+    id 'io.nextflow.nextflow-plugin' version "${nextflowPluginVersion}"
+    id 'java-test-fixtures'
+}
+
+nextflowPlugin {
+    nextflowVersion = '26.03.4-edge'
+
+    provider = "${nextflowPluginProvider}"
+    description = 'Provides dynamic container building and augmentation capabilities with on-demand software installation and advanced container management features'
+    className = 'io.seqera.wave.plugin.WavePlugin'
+    useDefaultDependencies = false
+    generateSpec = false
+    extensionPoints = [
+        'io.seqera.wave.plugin.WaveFactory',
+        'io.seqera.wave.plugin.config.WaveConfig',
+        'io.seqera.wave.plugin.resolver.WaveContainerResolver',
+    ]
+}
+
+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 = []
+}
+
+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 {
+    compileOnly project(':nextflow')
+    compileOnly 'org.slf4j:slf4j-api:2.0.17'
+    compileOnly 'org.pf4j:pf4j:3.14.1'
+    compileOnly 'io.seqera:lib-trace:0.1.0'
+    compileOnly 'io.seqera:lib-httpx:2.1.0'
+    compileOnly 'org.apache.commons:commons-lang3:3.18.0'
+
+    // Force lib-httpx version to avoid conflicts with older versions from nf-commons
+    testImplementation 'io.seqera:lib-httpx:2.1.0'
+
+    api 'org.apache.commons:commons-compress:1.26.1'
+    api 'com.google.code.gson:gson:2.13.1'
+    api 'org.yaml:snakeyaml:2.2'
+    api 'io.seqera:wave-api:1.31.1'
+    api 'io.seqera:wave-utils:1.31.1'
+
+    testImplementation(testFixtures(project(":nextflow")))
+    testImplementation "org.apache.groovy:groovy:4.0.31"
+    testImplementation "org.apache.groovy:groovy-nio:4.0.31"
+}