Merge branch 'main' into features/required-version

docs/resources.md

@@ -9,6 +9,22 @@ This page collects videos and blog posts about nf-test created by the community.
 
 ---
 
+### :material-tooltip-text:{ style="color: #337ab7" } Training Module: Hello nf-test
+
+This training modules introduces nf-test in a simple and easy to follow-along hello-nextflow style aimed for beginners.
+
+[hello nf-test training module](https://training.nextflow.io/hello_nextflow/05_hello_nf-test/)
+
+---
+
+### :material-tooltip-text:{ style="color: #337ab7" } Blog post: Leveraging nf-test for enhanced quality control in nf-core
+
+Reproducibility is an important attribute of all good science. This is specially true in the realm of bioinformatics, where software is hopefully being constantly updated, and pipelines are ideally being maintained. This blog post covers nf-test in the nf-core context.
+
+[Read blog post](https://nextflow.io/blog/2024/nf-test-in-nf-core.html)
+
+---
+
 ### :fontawesome-brands-youtube:{ style="color: #EE0F0F" } nf-core/bytesize: Converting pytest modules to nf-test
 
 **Adam Talbot** & **Sateesh Peri** do a live demo of converting nf-core DSL2 modules pytests to nf-test

pom.xml

@@ -4,7 +4,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>com.askimed</groupId>
 	<artifactId>nf-test</artifactId>
-	<version>0.8.3</version>
+	<version>0.8.4</version>
 	<name>nf-test</name>
 	<description>Simple test framework for Nextflow pipelines</description>
 	<url>https://github.com/askimed/nf-test</url>

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 = "0.8.3";
+	public static final String VERSION = "0.8.4";
 
 	public static final String PACKAGE =  "com.askimed.nf.test";
 

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

@@ -95,17 +95,26 @@ public File getConfig() {
 		return config;
 	}
 
-	@Override
-	public void setup(Config config, File testDirectory) throws IOException {
+	public void defineDirectories(File testDirectory) throws IOException {
 
 		if (testDirectory == null) {
 			throw new IOException("Testcase setup failed: No home directory set");
 		}
 
-		launchDir = initDirectory("Launch Directory", testDirectory, DIRECTORY_TESTS, getHash());
-		metaDir = initDirectory("Meta Directory", launchDir, DIRECTORY_META);
-		outputDir = initDirectory("Output Directory", launchDir, DIRECTORY_OUTPUT);
-		workDir = initDirectory("Working Directory", launchDir, DIRECTORY_WORK);
+		launchDir = constructDirectory(testDirectory, DIRECTORY_TESTS, getHash());
+		metaDir = constructDirectory(launchDir, DIRECTORY_META);
+		outputDir = constructDirectory(launchDir, DIRECTORY_OUTPUT);
+		workDir = constructDirectory(launchDir, DIRECTORY_WORK);
+
+	}
+
+	@Override
+	public void setup(Config config) throws IOException {
+
+		initDirectory("Launch Directory", launchDir);
+		initDirectory("Meta Directory", metaDir);
+		initDirectory("Output Directory", outputDir);
+		initDirectory("Working Directory", workDir);
 		FileStaging[] sharedDirectories = new FileStaging[]{
 				new FileStaging("bin", config != null ? config.getStageMode() : FileStaging.MODE_COPY),
 				new FileStaging("lib",  config != null ? config.getStageMode() : FileStaging.MODE_COPY),
@@ -136,15 +145,17 @@ public void execute() throws Throwable {
 		}
 	}
 
-	public File initDirectory(String name, File root, String... childs) throws IOException {
-
+	public File constructDirectory(File root, String... childs) {
 		String path = FileUtil.path(root.getAbsolutePath(), FileUtil.path(childs));
-
 		File directory = new File(path).getAbsoluteFile();
+		return directory;
+	}
+
+	public void initDirectory(String name, File directory) throws IOException {
+
 		try {
 			FileUtil.deleteDirectory(directory);
 			FileUtil.createDirectory(directory);
-			return directory;
 		} catch (Exception e) {
 			throw new IOException(name + " '" + directory + "' could not be deleted or created:\n" + e);
 		}

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

@@ -82,14 +82,19 @@ public void evalualteTestClosures() throws Throwable {
 			Closure closure = namedClosure.closure;
 
 			ITest test = getNewTestInstance(testName);
-			test.setup(config, getHomeDirectory());
+			test.defineDirectories(getHomeDirectory());
 			closure.setDelegate(test);
 			closure.setResolveStrategy(Closure.DELEGATE_ONLY);
 			closure.call();
 			addTest(test);
 		}
 	}
 
+	public void setupTest(ITest test) throws Throwable {
+		test.setup(config);
+	}
+
+
 	protected abstract ITest getNewTestInstance(String name);
 
 	public void setScript(String script) {

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

@@ -6,7 +6,9 @@
 
 public interface ITest extends ITaggable {
 
-	public void setup(Config config, File homeDirectory) throws Throwable;
+	public void defineDirectories(File testDirectory) throws Throwable;
+
+	public void setup(Config config) throws Throwable;
 
 	public void execute() throws Throwable;
 

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

@@ -36,4 +36,6 @@ public interface ITestSuite extends ITaggable {
 
 	public void evalualteTestClosures() throws Throwable;
 
-}
+	public void setupTest(ITest test) throws Throwable;
+
+}

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

@@ -199,6 +199,8 @@ public int execute() throws Throwable {
 				log.info("Run test '{}'. type: {}", test, test.getClass().getName());
 				totalTests++;
 
+				testSuite.setupTest(test);
+
 				listener.executionStarted(test);
 				TestExecutionResult result = new TestExecutionResult(test);
 				test.setWithTrace(withTrace);