Add support of relative paths for script definition (#103)

* Add support of relative paths for script definition

* Add relative paths to documentation

.gitignore

@@ -10,4 +10,4 @@ output
 test_mock.nf
 /.nf-test/
 site
-tests
+/tests

docs/docs/testcases/nextflow_function.md

@@ -15,6 +15,9 @@ nextflow_function {
 }
 ```
 
+>:bulb: Script paths that start with `./` or `../` are considered relative paths. These paths are resolved based on the location of the test script. Relative paths are beneficial when you want to reference files or directories located within the same directory as your test script or in a parent directory. These paths provide a convenient way to access files without specifying the entire path.
+
+
 ### Multiple Functions
 
 If a Nextflow script contains multiple functions and you want to test them all in the same testsuite, you can override the `function` property in each test. For example:

docs/docs/testcases/nextflow_process.md

@@ -16,6 +16,9 @@ nextflow_process {
 }
 ```
 
+
+>:bulb: Script paths that start with `./` or `../` are considered relative paths. These paths are resolved based on the location of the test script. Relative paths are beneficial when you want to reference files or directories located within the same directory as your test script or in a parent directory. These paths provide a convenient way to access files without specifying the entire path.
+
 ## Assertions
 
 The `process` object can be used in asserts to check its status or error messages.
@@ -52,6 +55,19 @@ assert process.out.my_channel.size() == 3
 assert process.out.my_channel.get(0) == "hello"
 ```
 
+Channels that lack explicit names can be addressed using square brackets and the corresponding index. This indexing method provides a straightforward way to interact with channels without the need for predefined names. To access the first output channel, you can use the index [0] as demonstrated below:
+
+```Groovy
+// channel exists
+assert process.out[0] != null
+
+// channel contains 3 elements
+assert process.out[0].size() == 3
+
+// first element is "hello"
+assert process.out[0].get(0) == "hello"
+````
+
 ## Example
 
 ### Nextflow script

docs/docs/testcases/nextflow_workflow.md

@@ -1,6 +1,9 @@
 # Workflow Testing
+
 nf-test also allows to test a specific workflow. Please checkout the [CLI](../cli/generate.md) to generate a workflow test.
+
 ## Syntax
+
 ```Groovy
 nextflow_workflow {
 
@@ -14,6 +17,9 @@ nextflow_workflow {
 }
 ```
 
+> :bulb: Script paths that start with `./` or `../` are considered relative paths. These paths are resolved based on the location of the test script. Relative paths are beneficial when you want to reference files or directories located within the same directory as your test script or in a parent directory. These paths provide a convenient way to access files without specifying the entire path.
+
+
 ## Assertions
 
 The `workflow` object can be used in asserts to check its status, error messages or traces.
@@ -42,6 +48,21 @@ assert workflow.stdout.contains("Hello World") == 3
 
 ```
 
+### Output Channels
+
+The `workflow.out` object provides access to the content of all named output Channels (see Nextflow `emit`):
+
+```groovy
+// channel exists
+assert workflow.out.my_channel != null
+
+// channel contains 3 elements
+assert workflow.out.my_channel.size() == 3
+
+// first element is "hello"
+assert workflow.out.my_channel.get(0) == "hello"
+```
+
 
 ## Example
 

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

@@ -23,6 +23,8 @@ public abstract class AbstractTestSuite implements ITestSuite {
 	private boolean autoSort = true;
 
 	private String options = "";
+
+	private String directory = "";
 
 	private List<String> tags = new Vector<String>();
 
@@ -96,13 +98,19 @@ public File getLocalConfig() {
 	@Override
 	public void setFilename(String filename) {
 		this.filename = filename;
+		this.directory = new File(filename).getParentFile().getAbsolutePath();
 	}
 
 	@Override
 	public String getFilename() {
 		return filename;
 	}
 
+	@Override
+	public String getDirectory() {
+		return directory;
+	}
+
 	@Override
 	public List<ITest> getTests() {
 		return tests;
@@ -127,4 +135,12 @@ public ITaggable getParent() {
 		return null;
 	}
 
+	protected String makeAbsolute(String path) {
+		return new File(directory, path).getAbsolutePath();
+	}
+
+	protected boolean isRelative(String path) {
+		return path.startsWith("../") || path.startsWith("./");
+	}
+
 }

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

@@ -18,6 +18,8 @@ public interface ITestSuite extends ITaggable {
 	public void setFilename(String filename);
 
 	public String getFilename();
+
+	public String getDirectory();
 
 	public void configure(Config config);
 

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

@@ -28,7 +28,11 @@ public void setFunction(String function) {
 	}
 
 	public String getScript() {
-		return script;
+		if (script != null && isRelative(script)) {
+			return makeAbsolute(script);
+		} else {
+			return script;
+		}
 	}
 
 	public void setScript(String script) {

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

@@ -14,7 +14,11 @@ public void script(String script) {
 	}
 
 	public String getScript() {
-		return script;
+		if (script != null && isRelative(script)) {
+			return makeAbsolute(script);
+		} else {
+			return script;
+		}
 	}
 
 	public void setScript(String script) {

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

@@ -28,7 +28,11 @@ public String getProcess() {
 	}
 
 	public String getScript() {
-		return script;
+		if (script != null && isRelative(script)) {
+			return makeAbsolute(script);
+		} else {
+			return script;
+		}
 	}
 
 	public void setScript(String script) {

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

@@ -28,7 +28,11 @@ public String getWorkflow() {
 	}
 
 	public String getScript() {
-		return script;
+		if (script != null && isRelative(script)) {
+			return makeAbsolute(script);
+		} else {
+			return script;
+		}
 	}
 
 	public void setScript(String script) {

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

@@ -169,4 +169,23 @@ public void testLoadGzip() throws Exception {
 		assertEquals(0, exitCode);
 
 	}
+
+	@Test
+	public void testScriptWithRelativePath() throws Exception {
+
+		App app = new App();
+		int exitCode = app.run(new String[] { "test", "test-data/process/default/test_process_relative.nf.test" });
+		assertEquals(0, exitCode);
+
+	}
+
+	@Test
+	public void testScriptWithRelativePathInSubfolder() throws Exception {
+
+		App app = new App();
+		int exitCode = app.run(new String[] { "test", "test-data/process/default/tests/test_process_relative.nf.test" });
+		assertEquals(0, exitCode);
+
+	}
+
 }

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

@@ -34,6 +34,15 @@ public void testWorkflowSucces() throws Exception {
 		assertEquals(0, exitCode);
 
 	}
+
+	@Test
+	public void testWorkflowWithRelativePath() throws Exception {
+
+		App app = new App();
+		int exitCode = app.run(new String[] { "test", "test-data/workflow/default/tests/trial.nf.test" });
+		assertEquals(0, exitCode);
+
+	}
 
 	@Test
 	public void testWorkflowWithNoOutputs() throws Exception {
@@ -57,7 +66,7 @@ public void testOverrideWorkflow() throws Exception {
 	public void testLibs() throws Exception {
 
 		App app = new App();
-		int exitCode = app.run(new String[] { "test", "test-data/workflow/libs/hello.nf.test", "--lib", "lib" });
+		int exitCode = app.run(new String[] { "test", "test-data/workflow/libs/hello.nf.test", "--lib", "lib" ,"--debug"});
 		assertEquals(0, exitCode);
 
 	}

test-data/process/default/test_process_relative.nf.test

@@ -0,0 +1,40 @@
+nextflow_process {
+
+  name "Test process xy"
+
+  script "./test_process.nf"
+  process "TEST_PROCESS"
+
+  test("Should create 5 files") {
+
+    when {
+      params {
+        outdir = "$outputDir/seb7"
+      }
+      process {
+        """
+        input[0] = Channel.of(1..5)
+        input[1] = "test"
+        """
+      }
+    }
+
+    then {
+      assert process.success
+      assert process.out.my_output_numbers == [1,2,3,4,5]      
+
+      assert process.out.my_output_files
+      assert process.out.my_output_files.size() == 5
+      def file1 = path process.out.my_output_files.get(0)
+      assert file1.fileName.toString() == "1_test.txt"
+      assert file1.fileName.toString().endsWith("test.txt")
+      assert file1.readLines() == ['lukas forer']
+
+      assert process.out.my_output_tuple
+      assert process.out.my_output_tuple.size() == 5
+      assert process.out.my_output_tuple.get(0).size() == 3
+    }
+
+  }
+
+}

test-data/process/default/tests/test_process_relative.nf.test

@@ -0,0 +1,40 @@
+nextflow_process {
+
+  name "Test process xy"
+
+  script "../test_process.nf"
+  process "TEST_PROCESS"
+
+  test("Should create 5 files") {
+
+    when {
+      params {
+        outdir = "$outputDir/seb7"
+      }
+      process {
+        """
+        input[0] = Channel.of(1..5)
+        input[1] = "test"
+        """
+      }
+    }
+
+    then {
+      assert process.success
+      assert process.out.my_output_numbers == [1,2,3,4,5]      
+
+      assert process.out.my_output_files
+      assert process.out.my_output_files.size() == 5
+      def file1 = path process.out.my_output_files.get(0)
+      assert file1.fileName.toString() == "1_test.txt"
+      assert file1.fileName.toString().endsWith("test.txt")
+      assert file1.readLines() == ['lukas forer']
+
+      assert process.out.my_output_tuple
+      assert process.out.my_output_tuple.size() == 5
+      assert process.out.my_output_tuple.get(0).size() == 3
+    }
+
+  }
+
+}

test-data/workflow/default/tests/trial.nf.test

@@ -0,0 +1,26 @@
+nextflow_workflow {
+
+    name "Test workflow"
+    script "../trial.nf"
+    workflow "trial"
+
+    test("Should run without failures") {
+        when {
+            params {
+                outdir = "tests/results"
+            }
+            workflow {
+                """
+                input[0] = Channel.of('a','b')
+                """
+            }
+        }
+
+        then {
+            //check if test case succeeded
+            assert workflow.success
+            assert workflow.out.lukas.size() == 2
+            assert workflow.out.sebastian.size() == 2
+        }
+    }
+}