Enable the execution of dependent modules for generating test data

docs/docs/testcases/setup.md

@@ -0,0 +1,155 @@
+# Setup Method
+
+The setup method allows you to specify processes or workflows that need to be executed before the primary `when` block. It serves as a mechanism to prepare the required input data or set up essential steps prior to the primary processing block.
+
+## Syntax
+
+The setup method is typically used within the context of a test case. The basic syntax for the setup method is as follows:
+
+```groovy
+test("my test"){
+    setup {
+        // Define and execute dependent processes or workflows here
+    }
+}
+```
+
+Within the setup block, you can use the `run` method to define and execute dependent processes or workflows.
+
+The `run` method syntax for a process is as follows:
+
+```groovy
+run("ProcessName") {
+    script "path/to/process/script.nf"
+    process {
+        // Define the process inputs here
+    }
+}
+```
+
+The `run` method syntax for a workflow is as follows:
+
+```groovy
+run("WorkflowName") {
+    script "path/to/workflow/script.nf"
+    workflow {
+        // Define the workflow inputs here
+    }
+}
+```
+
+!!! warning
+
+    Please keep in mind that changes in procsses or workflows, which are executed in the setup method, can result in a failed test run.
+
+## Example Usage
+
+### 1. Local Setup Method
+
+In this example, we create a setup method within a Nextflow process definition to execute a dependent process named "ABRICATE_RUN." This process generates input data that is required for the primary process "ABRICATE_SUMMARY." The `setup` block specifies the execution of "ABRICATE_RUN," and the `when` block defines the processing logic for "ABRICATE_SUMMARY."
+
+```groovy
+nextflow_process {
+
+    name "Test process data"
+
+    script "../main.nf"
+    process "ABRICATE_SUMMARY"
+    config "./nextflow.config"
+
+    test("Should use process ABRICATE_RUN to generate input data") {
+
+        setup {
+
+            run("ABRICATE_RUN") {
+                script "../../run/main.nf"
+                process {
+                    """
+                    input[0] =  Channel.fromList([
+                        tuple([ id:'test1', single_end:false ], // meta map
+                            file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)),
+                        tuple([ id:'test2', single_end:false ],
+                            file(params.test_data['haemophilus_influenzae']['genome']['genome_fna_gz'], checkIfExists: true))
+                    ])
+                    """
+                }
+            }
+
+        }
+
+        when {
+            process {
+                """
+                input[0] = ABRICATE_RUN.out.report.collect{ meta, report -> report }.map{ report -> [[ id: 'test_summary'], report]}
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+        }
+    }
+
+}
+```
+
+### 2. Global Setup Method
+
+In this example, a global setup method is defined for all tests within a Nextflow process definition. The setup method is applied to multiple test cases, ensuring consistent setup for each test. This approach is useful when multiple tests share the same setup requirements.
+
+```groovy
+nextflow_process {
+
+    name "Test process data"
+
+    script "../main.nf"
+    process "ABRICATE_SUMMARY"
+    config "./nextflow.config"
+
+    setup {
+        run("ABRICATE_RUN") {
+            script "../../run/main.nf"
+            process {
+                """
+                input[0] =  Channel.fromList([
+                    tuple([ id:'test1', single_end:false ], // meta map
+                        file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)),
+                    tuple([ id:'test2', single_end:false ],
+                        file(params.test_data['haemophilus_influenzae']['genome']['genome_fna_gz'], checkIfExists: true))
+                ])
+                """
+            }
+        }
+    }
+
+    test("first test") {
+        when {
+            process {
+                """
+                input[0] = ABRICATE_RUN.out.report.collect{ meta, report -> report }.map{ report -> [[ id: 'test_summary'], report]}
+                """
+            }
+        }
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+        }
+    }
+
+    test("second test") {
+        when {
+            process {
+                """
+                input[0] = ABRICATE_RUN.out.report.collect{ meta, report -> report }.map{ report -> [[ id: 'test_summary'], report]}
+                """
+            }
+        }
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+        }
+    }
+
+}
+```

mkdocs.yml

@@ -4,16 +4,16 @@ copyright: "© 2021 - 2023 Lukas Forer and Sebastian Schönherr"
 theme:
   name: material
   features:
-      - content.tooltips
-      #- navigation.expand
-      - navigation.footer
-      - navigation.tabs
-      #- navigation.tabs.sticky
-      - search.highlight
-      - search.share
-      - search.suggest
-      - toc.integrate
-      - content.tabs.link
+    - content.tooltips
+    #- navigation.expand
+    - navigation.footer
+    - navigation.tabs
+    #- navigation.tabs.sticky
+    - search.highlight
+    - search.share
+    - search.suggest
+    - toc.integrate
+    - content.tabs.link
   font:
     text: Segoe UI
 
@@ -36,44 +36,44 @@ nav:
   - Home: index.md
   - Installation: installation.md
   - Documentation:
-    - Getting Started: docs/getting-started.md
-    - Writing Tests:
-      - Pipeline Testing: docs/testcases/nextflow_pipeline.md
-      - Workflow Testing: docs/testcases/nextflow_workflow.md
-      - Process Testing: docs/testcases/nextflow_process.md
-      - Function Testing: docs/testcases/nextflow_function.md
-      - Params Dictionary: docs/testcases/params.md
-      - Global Variables: docs/testcases/global_variables.md      
-    - Running Tests: docs/running-tests.md
-    - Writing Assertions:
-      - Power Assertions: docs/assertions/assertions.md
-      - Files: docs/assertions/files.md
-      - Snapshots: docs/assertions/snapshots.md
-      - Regular Expressions: docs/assertions/regular-expressions.md
-      - FASTA Files: docs/assertions/fasta.md
-      - Using Third-Party Libraries: docs/assertions/libraries.md
-    - Command Line Interface (CLI):
-      - init: docs/cli/init.md
-      - generate: docs/cli/generate.md
-      - test: docs/cli/test.md
-      - list: docs/cli/list.md
-      - clean: docs/cli/clean.md
-    - Configuration: docs/configuration.md
-    - Plugins:
-      - Available Plugins: https://code.askimed.com/nf-test-plugins
-      - Using Plugins: docs/plugins/using-plugins.md
-      - Developing Plugins: docs/plugins/developing-plugins.md
+      - Getting Started: docs/getting-started.md
+      - Writing Tests:
+          - Pipeline Testing: docs/testcases/nextflow_pipeline.md
+          - Workflow Testing: docs/testcases/nextflow_workflow.md
+          - Process Testing: docs/testcases/nextflow_process.md
+          - Function Testing: docs/testcases/nextflow_function.md
+          - Params Dictionary: docs/testcases/params.md
+          - Setup Method: docs/testcases/setup.md
+          - Global Variables: docs/testcases/global_variables.md
+      - Running Tests: docs/running-tests.md
+      - Writing Assertions:
+          - Power Assertions: docs/assertions/assertions.md
+          - Files: docs/assertions/files.md
+          - Snapshots: docs/assertions/snapshots.md
+          - Regular Expressions: docs/assertions/regular-expressions.md
+          - FASTA Files: docs/assertions/fasta.md
+          - Using Third-Party Libraries: docs/assertions/libraries.md
+      - Command Line Interface (CLI):
+          - init: docs/cli/init.md
+          - generate: docs/cli/generate.md
+          - test: docs/cli/test.md
+          - list: docs/cli/list.md
+          - clean: docs/cli/clean.md
+      - Configuration: docs/configuration.md
+      - Plugins:
+          - Available Plugins: https://code.askimed.com/nf-test-plugins
+          - Using Plugins: docs/plugins/using-plugins.md
+          - Developing Plugins: docs/plugins/developing-plugins.md
   - Resources: resources.md
   - About: about.md
 
-
 markdown_extensions:
   - admonition
   - pymdownx.details
   - pymdownx.superfences
   - pymdownx.tabbed:
-      alternate_style: true 
+      alternate_style: true
   - attr_list
   - pymdownx.emoji:
       emoji_index: !!python/name:materialx.emoji.twemoji
-      emoji_generator: !!python/name:materialx.emoji.to_svg 
+      emoji_generator: !!python/name:materialx.emoji.to_svg

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

@@ -84,7 +84,14 @@ public AbstractTest(AbstractTestSuite parent) {
 	}
 
 	public void config(String config) {
-		this.config = new File(config);
+		if (config == null) {
+			return;
+		}
+		if (parent.isRelative(config)) {
+			this.config = new File(parent.makeAbsolute(config));
+		} else {
+			this.config = new File(config);
+		}
 	}
 
 	public File getConfig() {

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

@@ -20,7 +20,7 @@ public abstract class AbstractTestSuite implements ITestSuite {
 
 	private File globalConfig = null;
 
-	private File localConfig = null;
+	private String localConfig = null;
 
 	private List<ITest> tests = new Vector<ITest>();
 
@@ -62,7 +62,7 @@ public void script(String script) {
 	}
 
 	public String getScript() {
-		if (script != null && isRelative(script)) {
+		if (isRelative(script)) {
 			return makeAbsolute(script);
 		} else {
 			return script;
@@ -105,7 +105,7 @@ public void profile(String profile) {
 	}
 
 	public void config(String config) {
-		this.localConfig = new File(config);
+		this.localConfig = config;
 	}
 
 	public void setName(String name) {
@@ -159,12 +159,15 @@ public File getGlobalConfigFile() {
 		return globalConfig;
 	}
 
-	public void setLocalConfig(File localConfig) {
-		this.localConfig = localConfig;
-	}
-
 	public File getLocalConfig() {
-		return localConfig;
+		if (localConfig == null) {
+			return null;
+		}
+		if (isRelative(localConfig)) {
+			return new File(makeAbsolute(localConfig));
+		} else {
+			return new File(localConfig);
+		}
 	}
 
 	public File getHomeDirectory() {
@@ -243,11 +246,14 @@ public boolean hasFailedTests() {
 		return failedTests;
 	}
 
-	protected String makeAbsolute(String path) {
+	public String makeAbsolute(String path) {
 		return new File(directory, path).getAbsolutePath();
 	}
 
-	protected boolean isRelative(String path) {
+	public boolean isRelative(String path) {
+		if (path == null) {
+			return false;
+		}
 		return path.startsWith("../") || path.startsWith("./");
 	}