Merge branch 'main' into features/dependencies

docs/docs/cli/test.md

@@ -12,9 +12,9 @@ nf-test test [<NEXTFLOW_FILES>|<SCRIPT_FOLDERS>]
 
 To run your test using a specific Nextflow profile, you can use the `--profile` argument. [Learn more](/docs/configuration/#managing-profiles).
 
-#### `--debug`
+#### `--verbose`
 
-The debug parameter prints out all available output channels which can be accessed in the `then` clause.
+Prints out the Nextflow output during test runs.
 
 #### `--without-trace`
 
@@ -32,6 +32,10 @@ Writes test results in [TAP format](https://testanything.org) to file.
 
 Writes test results in [JUnit XML format](https://junit.org/) to file, which conforms to [the standard schema](https://github.com/junit-team/junit5/blob/242f3b3ef84cfd96c9de26992588812a68cdef8b/platform-tests/src/test/resources/jenkins-junit.xsd).
 
+#### `--debug`
+
+The debug parameter prints out debugging messages and all available output channels which can be accessed in the `then` clause.
+
 ## Examples
 
 - Run all test scripts that can be found in the `testDir` defined in the `nf-test.config` file in the current working directory:

src/main/java/com/askimed/nf/test/commands/RunTestsCommand.java

@@ -22,6 +22,7 @@
 import com.askimed.nf.test.core.reports.TapTestReportWriter;
 import com.askimed.nf.test.core.reports.XmlReportWriter;
 import com.askimed.nf.test.lang.TestSuiteBuilder;
+import com.askimed.nf.test.nextflow.NextflowCommand;
 import com.askimed.nf.test.plugins.PluginManager;
 import com.askimed.nf.test.util.AnsiColors;
 
@@ -37,9 +38,13 @@ public class RunTestsCommand extends AbstractCommand {
 	private List<File> testPaths = new ArrayList<File>();
 
 	@Option(names = {
-			"--debug" }, description = "Show Nextflow output", required = false, showDefaultValue = Visibility.ALWAYS)
+			"--debug" }, description = "Show debugging infos and dump channels", required = false, showDefaultValue = Visibility.ALWAYS)
 	private boolean debug = false;
 
+	@Option(names = {
+			"--verbose" }, description = "Show Nextflow output", required = false, showDefaultValue = Visibility.ALWAYS)
+	private boolean verbose = false;
+
 	@Option(names = {
 			"--profile" }, description = "Profile to execute all tests", required = false, showDefaultValue = Visibility.ALWAYS)
 	private String profile = null;
@@ -155,6 +160,8 @@ public Integer execute() throws Exception {
 				listener.addListener(new XmlReportWriter(junitXml));
 			}
 
+			NextflowCommand.setVerbose(verbose);
+
 			TagQuery tagQuery = new TagQuery(tags);
 
 			TestExecutionEngine engine = new TestExecutionEngine();

src/main/java/com/askimed/nf/test/lang/function/FunctionTest.java

@@ -138,7 +138,7 @@ public void execute() throws Throwable {
 		}
 		nextflow.setOut(outFile);
 		nextflow.setErr(errFile);
-		nextflow.setSilent(!isDebug());
+		nextflow.setDebug(isDebug());
 		nextflow.setLog(logFile);
 		nextflow.setLaunchDir(launchDir);
 		nextflow.setWorkDir(workDir);

src/main/java/com/askimed/nf/test/lang/pipeline/PipelineTest.java

@@ -66,7 +66,7 @@ public void then(@DelegatesTo(value = PipelineTest.class, strategy = Closure.DEL
 	public void execute() throws Throwable {
 
 		super.execute();
-		
+
 		context.init(this);
 
 		if (setup != null) {
@@ -94,21 +94,21 @@ public void execute() throws Throwable {
 		if (!script.startsWith("/") && !script.startsWith("./")) {
 			script = new File(script).getAbsolutePath();
 		}
-		
-		//file not found. try as github location
+
+		// file not found. try as github location
 		if (!new File(script).exists()) {
 			script = parent.getScript();
 		}
-		
+
 		NextflowCommand nextflow = new NextflowCommand();
 		nextflow.setScript(script);
 		nextflow.setParams(context.getParams());
-		for (String profile: parent.getProfiles()) {
+		for (String profile : parent.getProfiles()) {
 			nextflow.addProfile(profile);
 		}
 		File projectConfig = new File("nextflow.config");
 		if (projectConfig.exists()) {
-			nextflow.addConfig(projectConfig);	
+			nextflow.addConfig(projectConfig);
 		}
 		nextflow.addConfig(parent.getGlobalConfigFile());
 		nextflow.addConfig(parent.getLocalConfig());
@@ -118,7 +118,7 @@ public void execute() throws Throwable {
 		}
 		nextflow.setOut(outFile);
 		nextflow.setErr(errFile);
-		nextflow.setSilent(!isDebug());
+		nextflow.setDebug(isDebug());
 		nextflow.setLog(logFile);
 		nextflow.setLaunchDir(launchDir);
 		nextflow.setWorkDir(workDir);

src/main/java/com/askimed/nf/test/lang/process/ProcessTest.java

@@ -141,7 +141,7 @@ public void execute() throws Throwable {
 		}
 		nextflow.setOut(outFile);
 		nextflow.setErr(errFile);
-		nextflow.setSilent(!isDebug());
+		nextflow.setDebug(isDebug());
 		nextflow.setLog(logFile);
 		nextflow.setLaunchDir(launchDir);
 		nextflow.setWorkDir(workDir);

src/main/java/com/askimed/nf/test/lang/workflow/WorkflowTest.java

@@ -153,7 +153,7 @@ public void execute() throws Throwable {
 		}
 		nextflow.setOut(outFile);
 		nextflow.setErr(errFile);
-		nextflow.setSilent(!isDebug());
+		nextflow.setDebug(isDebug());
 		nextflow.setLog(logFile);
 		nextflow.setLaunchDir(launchDir);
 		nextflow.setWorkDir(workDir);

src/main/java/com/askimed/nf/test/nextflow/NextflowCommand.java

@@ -8,7 +8,6 @@
 import java.nio.file.Files;
 import java.util.List;
 import java.util.Map;
-import java.util.StringJoiner;
 import java.util.Vector;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
@@ -36,7 +35,7 @@ public class NextflowCommand {
 
 	private File launchDir;
 
-	private boolean silent = true;
+	private boolean debug = false;
 
 	private File trace = null;
 
@@ -48,6 +47,8 @@ public class NextflowCommand {
 
 	private String options = "";
 
+	private static boolean verbose = false;
+
 	public static String ERROR = "Nextflow Binary not found. Please check if Nextflow is in a directory accessible by your $PATH variable or set $NEXTFLOW_HOME.";
 
 	public NextflowCommand() {
@@ -86,8 +87,12 @@ public void setParams(Map<String, Object> params) {
 		this.params = params;
 	}
 
-	public void setSilent(boolean silent) {
-		this.silent = silent;
+	public void setDebug(boolean debug) {
+		this.debug = debug;
+	}
+
+	public static void setVerbose(boolean verbose) {
+		NextflowCommand.verbose = verbose;
 	}
 
 	public void setTrace(File trace) {
@@ -168,7 +173,9 @@ public int execute() throws IOException {
 		writeParamsJson(params, paramsFile);
 
 		List<String> args = new Vector<String>();
-		args.add("-quiet");
+		if (!verbose) {
+			args.add("-quiet");
+		}
 		if (log != null) {
 			args.add("-log");
 			args.add(log.getAbsolutePath());
@@ -203,26 +210,30 @@ public int execute() throws IOException {
 			nextflow.setDirectory(launchDir.getAbsolutePath());
 		}
 		nextflow.setParams(args);
-		nextflow.setSilent(true);
+		if (verbose) {
+			System.out.println("");
+		}
+		nextflow.setSilent(!verbose);
 		if (out != null) {
 			nextflow.saveStdOut(out.getAbsolutePath());
 		}
 		if (err != null) {
 			nextflow.saveStdErr(err.getAbsolutePath());
 		}
-		if (!silent) {
-			System.out.println();
-			System.out.println("    Nextflow:");
-			System.out.println("       Profiles: " + profiles);
-			System.out.println("       Configs: " + configs);
-			System.out.println("       Command: " + nextflow.getExecutedCommand());
+		if (debug) {
+			//System.out.println();
+			System.out.println("    Profiles: " + profiles);
+			System.out.println("    Configs: " + configs);
+			System.out.println("    Command: " + nextflow.getExecutedCommand());
 		}
 
 		int result = nextflow.execute();
-
-		if (!silent) {
+		if (debug) {
 			printDebugInfo();
 		}
+		if (verbose || debug) {
+			System.out.print("    ");
+		}
 		return result;
 
 	}

src/main/java/com/askimed/nf/test/util/CommandStreamHandler.java

@@ -48,7 +48,7 @@ public void run() {
 			while ((size = is.read(buffer)) > 0) {
 				if (!silent) {
 					String line = new String(buffer, 0, size);
-					System.out.println(line);
+					System.out.print("    > " + line);
 				}
 				if (save) {
 					writer.write(buffer, 0, size);