Update test strategy in github actions

.github/workflows/run-tests.yml

@@ -4,22 +4,24 @@ on: [push, pull_request]
 
 jobs:
   test:
-
     runs-on: ubuntu-latest
-
+    strategy:
+      matrix:
+        java: [ '11', '17', '21' ]
+        nextflow: ['latest-edge', 'latest-stable' ]
     steps:
       - name: Checkout
         uses: actions/checkout@v2
 
-      - name: Install JDK 11
+      - name: Install JDK ${{ matrix.java }}
         uses: actions/setup-java@v1
         with:
-          java-version: 11
+          java-version: ${{ matrix.java }}
 
-      - name: Install Nextflow v22.10.4
-        run: |
-          export NXF_VER=22.10.4;curl -s https://get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
+      - name: Setup Nextflow ${{ matrix.nextflow }}
+        uses: nf-core/setup-nextflow@v1
+        with:
+          version: "${{ matrix.nextflow }}"
 
       - name: Test
         run: mvn install

docs/CNAME

@@ -0,0 +1 @@
+www.nf-test.com

pom.xml

@@ -4,7 +4,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>com.askimed</groupId>
 	<artifactId>nf-test</artifactId>
-	<version>0.8.2</version>
+	<version>0.8.3</version>
 	<name>nf-test</name>
 	<description>Simple test framework for Nextflow pipelines</description>
 	<url>https://github.com/askimed/nf-test</url>
@@ -37,20 +37,20 @@
 		<dependency>
 			<groupId>org.codehaus.groovy</groupId>
 			<artifactId>groovy-all</artifactId>
-			<version>3.0.9</version>
+			<version>3.0.19</version>
 			<type>pom</type>
 		</dependency>
 
 		<dependency>
 			<groupId>org.codehaus.groovy</groupId>
 			<artifactId>groovy-nio</artifactId>
-			<version>3.0.9</version>
+			<version>3.0.19</version>
 		</dependency>
 
 		<dependency>
 			<groupId>org.codehaus.groovy</groupId>
 			<artifactId>groovy-yaml</artifactId>
-			<version>3.0.9</version>
+			<version>3.0.19</version>
 		</dependency>
 
 		<dependency>

src/main/java/com/askimed/nf/test/App.java

@@ -17,7 +17,7 @@ public class App {
 
 	public static final String NAME = "nf-test";
 
-	public static final String VERSION = "0.8.2";
+	public static final String VERSION = "0.8.3";
 
 	public static final String PACKAGE =  "com.askimed.nf.test";
 

src/main/java/com/askimed/nf/test/config/Config.java

@@ -38,6 +38,8 @@ public class Config {
 
 	private StageBuilder stageBuilder = new StageBuilder();
 
+	private String stageMode = FileStaging.MODE_COPY;
+
 	public void testsDir(String testsDir) {
 		this.testsDir = testsDir;
 	}
@@ -114,6 +116,18 @@ public String getLibDir() {
 		return libDir;
 	}
 
+	public void setStageMode(String stageMode) {
+		this.stageMode = stageMode;
+	}
+
+	public String getStageMode() {
+		return stageMode;
+	}
+
+	public void stageMode(String stageMode) {
+		this.stageMode = stageMode;
+	}
+
 	public void stage(Closure closure) {
 		closure.setDelegate(stageBuilder);
 		closure.setResolveStrategy(Closure.DELEGATE_ONLY);		

src/main/java/com/askimed/nf/test/core/AbstractTest.java

@@ -59,9 +59,6 @@ public abstract class AbstractTest implements ITest {
 
 	public boolean skipped = false;
 
-	public static FileStaging[] SHARED_DIRECTORIES = { new FileStaging("bin"), new FileStaging("lib"),
-			new FileStaging("assets") };
-
 	protected File config = null;
 
 	private boolean updateSnapshot = false;
@@ -109,10 +106,14 @@ public void setup(Config config, File testDirectory) throws IOException {
 		metaDir = initDirectory("Meta Directory", launchDir, DIRECTORY_META);
 		outputDir = initDirectory("Output Directory", launchDir, DIRECTORY_OUTPUT);
 		workDir = initDirectory("Working Directory", launchDir, DIRECTORY_WORK);
-
+		FileStaging[] sharedDirectories = new FileStaging[]{
+				new FileStaging("bin", config != null ? config.getStageMode() : FileStaging.MODE_COPY),
+				new FileStaging("lib",  config != null ? config.getStageMode() : FileStaging.MODE_COPY),
+				new FileStaging("assets", config != null ? config.getStageMode() : FileStaging.MODE_COPY)
+		};
 		try {
 			// copy bin, assets and lib to metaDir
-			shareDirectories(SHARED_DIRECTORIES, metaDir);
+			shareDirectories(sharedDirectories, metaDir);
 			if (config != null) {
 				// copy user defined staging directories
 				log.debug("Stage {} user provided files...", config.getStageBuilder().getPaths().size());