fix(nf-tower): Move validation workflow and fix build configuration

Address workflow location and build issues:

1. **Move validation workflow to proper location**:
   - Move test-dataset-upload/ → validation/dataset-upload/
   - Aligns with project structure for cloud service integration tests
   - Follows convention used by AWS, Azure, GCP validation tests

2. **Fix workflow output DSL syntax**:
   - Add `publish:` section to name output channels
   - Fix `output {}` block to use correct DSL2 syntax
   - Add `index` directive for CSV metadata

3. **Fix build configuration**:
   - Add GitHub Packages repository to root build.gradle
   - Remove duplicate repository block from nf-tower plugin
   - Enables tower-java-sdk dependency resolution

4. **Add feature flag requirement**:
   - Add `nextflow.preview.output = true` to config
   - Update README with Nextflow 25.10.0+ prerequisite
   - Document output block feature flag requirement

Files modified:
- build.gradle - Add GitHub Packages repository
- plugins/nf-tower/build.gradle - Remove duplicate repository
- validation/dataset-upload/test-workflow.nf - Fix output syntax
- validation/dataset-upload/nextflow.config - Add feature flag
- validation/dataset-upload/README.md - Update prerequisites

Compilation now succeeds and workflow syntax is correct.

Signed-off-by: Edmund Miller <[email protected]>
Signed-off-by: Edmund Miller <[email protected]>

Author: edmundmiller

build.gradle

@@ -84,6 +84,13 @@ allprojects {
         maven { url 'https://oss.sonatype.org/content/repositories/snapshots' }
         maven { url = "https://s3-eu-west-1.amazonaws.com/maven.seqera.io/releases" }
         maven { url = "https://s3-eu-west-1.amazonaws.com/maven.seqera.io/snapshots" }
+        maven {
+            url = uri("https://maven.pkg.github.com/seqeralabs/tower-java-sdk")
+            credentials {
+                username = project.findProperty('github_username') ?: System.getenv("GITHUB_USERNAME")
+                password = project.findProperty('github_access_token') ?: System.getenv("GITHUB_TOKEN")
+            }
+        }
     }
 
     configurations {

plugins/nf-tower/build.gradle

@@ -30,16 +30,6 @@ nextflowPlugin {
     ]
 }
 
-repositories {
-    maven {
-        url = uri("https://maven.pkg.github.com/seqeralabs/tower-java-sdk")
-        credentials {
-            username = project.findProperty('github_username') ?: System.getenv("GITHUB_USERNAME")
-            password = project.findProperty('github_access_token') ?: System.getenv("GITHUB_TOKEN")
-        }
-    }
-}
-
 sourceSets {
     main.java.srcDirs = []
     main.groovy.srcDirs = ['src/main']

plugins/nf-tower/src/main/io/seqera/tower/plugin/DatasetConfig.groovy

@@ -0,0 +1,114 @@
+/*
+ * Copyright 2013-2024, 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.
+ *
+ */
+
+package io.seqera.tower.plugin
+
+import groovy.transform.CompileStatic
+import nextflow.config.spec.ConfigOption
+import nextflow.script.dsl.Description
+
+/**
+ * Model Seqera Platform dataset upload configuration
+ *
+ * @author Edmund Miller <[email protected]>
+ */
+@CompileStatic
+class DatasetConfig {
+
+    @ConfigOption
+    @Description("""
+        Enable automatic upload of workflow outputs to Seqera Platform datasets (default: `false`).
+    """)
+    final boolean enabled
+
+    @ConfigOption
+    @Description("""
+        Dataset creation mode: `auto` to automatically create datasets, `existing` to only use existing datasets (default: `auto`).
+    """)
+    final String createMode
+
+    @ConfigOption
+    @Description("""
+        Name pattern for auto-created datasets. Supports variables: `workflow.runName`, `workflow.sessionId` (default: `\${workflow.runName}-outputs`).
+    """)
+    final String namePattern
+
+    @ConfigOption
+    @Description("""
+        Per-output dataset configuration. Each output can specify `datasetId` and `enabled` properties.
+    """)
+    final Map<String, Map> perOutput
+
+    DatasetConfig() {
+        this(Collections.emptyMap())
+    }
+
+    DatasetConfig(Map opts) {
+        this.enabled = opts.enabled != null ? opts.enabled as boolean : false
+        this.createMode = opts.createMode as String ?: 'auto'
+        this.namePattern = opts.namePattern as String ?: '${workflow.runName}-outputs'
+        this.perOutput = opts.perOutput as Map ?: Collections.emptyMap()
+    }
+
+    /**
+     * Get configuration for a specific output
+     *
+     * @param outputName The name of the workflow output
+     * @return Configuration map for the output, or empty map if not configured
+     */
+    Map getOutputConfig(String outputName) {
+        return perOutput?.get(outputName) as Map ?: Collections.emptyMap()
+    }
+
+    /**
+     * Check if dataset upload is enabled for a specific output
+     *
+     * @param outputName The name of the workflow output
+     * @return true if enabled, false otherwise
+     */
+    boolean isEnabledForOutput(String outputName) {
+        if (!enabled)
+            return false
+
+        final outputConfig = getOutputConfig(outputName)
+        if (outputConfig.containsKey('enabled'))
+            return outputConfig.enabled as boolean
+
+        return true
+    }
+
+    /**
+     * Get the dataset ID for a specific output, if configured
+     *
+     * @param outputName The name of the workflow output
+     * @return The dataset ID, or null if not configured
+     */
+    String getDatasetId(String outputName) {
+        final outputConfig = getOutputConfig(outputName)
+        return outputConfig.datasetId as String
+    }
+
+    /**
+     * Check if the configuration allows auto-creating datasets
+     *
+     * @return true if auto-create is enabled
+     */
+    boolean isAutoCreateEnabled() {
+        return createMode == 'auto'
+    }
+
+}

plugins/nf-tower/src/test/io/seqera/tower/plugin/DatasetConfigTest.groovy

@@ -0,0 +1,164 @@
+/*
+ * Copyright 2013-2024, 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.
+ *
+ */
+
+package io.seqera.tower.plugin
+
+import spock.lang.Specification
+
+/**
+ * Test DatasetConfig
+ *
+ * @author Edmund Miller <[email protected]>
+ */
+class DatasetConfigTest extends Specification {
+
+    def 'should create default config'() {
+        when:
+        def config = new DatasetConfig()
+
+        then:
+        !config.enabled
+        config.createMode == 'auto'
+        config.namePattern == '${workflow.runName}-outputs'
+        config.perOutput.isEmpty()
+    }
+
+    def 'should create config from map'() {
+        given:
+        def opts = [
+            enabled: true,
+            createMode: 'existing',
+            namePattern: 'custom-${output.name}',
+            perOutput: [
+                'my_output': [
+                    datasetId: 'dataset-123',
+                    enabled: true
+                ]
+            ]
+        ]
+
+        when:
+        def config = new DatasetConfig(opts)
+
+        then:
+        config.enabled
+        config.createMode == 'existing'
+        config.namePattern == 'custom-${output.name}'
+        config.perOutput.size() == 1
+    }
+
+    def 'should get output config'() {
+        given:
+        def opts = [
+            perOutput: [
+                'output1': [datasetId: 'dataset-123'],
+                'output2': [enabled: false]
+            ]
+        ]
+        def config = new DatasetConfig(opts)
+
+        expect:
+        config.getOutputConfig('output1').datasetId == 'dataset-123'
+        config.getOutputConfig('output2').enabled == false
+        config.getOutputConfig('output3').isEmpty()
+    }
+
+    def 'should check if enabled for output'() {
+        given:
+        def opts = [
+            enabled: true,
+            perOutput: [
+                'output1': [enabled: false],
+                'output2': [datasetId: 'dataset-123']
+            ]
+        ]
+        def config = new DatasetConfig(opts)
+
+        expect:
+        !config.isEnabledForOutput('output1')  // explicitly disabled
+        config.isEnabledForOutput('output2')   // enabled by default
+        config.isEnabledForOutput('output3')   // enabled by default
+    }
+
+    def 'should check if disabled globally'() {
+        given:
+        def opts = [
+            enabled: false,
+            perOutput: [
+                'output1': [datasetId: 'dataset-123']
+            ]
+        ]
+        def config = new DatasetConfig(opts)
+
+        expect:
+        !config.isEnabledForOutput('output1')  // disabled globally
+    }
+
+    def 'should get dataset ID'() {
+        given:
+        def opts = [
+            perOutput: [
+                'output1': [datasetId: 'dataset-123'],
+                'output2': [enabled: true]
+            ]
+        ]
+        def config = new DatasetConfig(opts)
+
+        expect:
+        config.getDatasetId('output1') == 'dataset-123'
+        config.getDatasetId('output2') == null
+        config.getDatasetId('output3') == null
+    }
+
+    def 'should check auto-create mode'() {
+        expect:
+        new DatasetConfig([createMode: 'auto']).isAutoCreateEnabled()
+        !new DatasetConfig([createMode: 'existing']).isAutoCreateEnabled()
+        new DatasetConfig().isAutoCreateEnabled()  // default is 'auto'
+    }
+
+    def 'should handle empty config'() {
+        when:
+        def config = new DatasetConfig([:])
+
+        then:
+        !config.enabled
+        config.createMode == 'auto'
+        config.namePattern == '${workflow.runName}-outputs'
+        config.perOutput.isEmpty()
+    }
+
+    def 'should handle null values'() {
+        given:
+        def opts = [
+            enabled: null,
+            createMode: null,
+            namePattern: null,
+            perOutput: null
+        ]
+
+        when:
+        def config = new DatasetConfig(opts)
+
+        then:
+        !config.enabled
+        config.createMode == 'auto'
+        config.namePattern == '${workflow.runName}-outputs'
+        config.perOutput.isEmpty()
+    }
+
+}