Merge branch 'main' into fixes/gzip-check

docs/docs/testcases/setup.md

@@ -38,6 +38,17 @@ run("WorkflowName") {
 }
 ```
 
+If you need to run the same process multiple times, you can set the alias of the process:
+
+```groovy
+run("GENERATE_DATA", alias: "MY_PROCESS") {
+    script "./generate_data.nf"
+    process {
+       ...
+    }
+}
+```
+
 !!! 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.
@@ -153,3 +164,61 @@ nextflow_process {
 
 }
 ```
+### 3. Aliasing of Dependencies
+
+In this example, the process `UNTAR` is used multiple times in the setup method:
+
+```groovy
+nextflow_process {
+
+    ...
+
+    setup {
+
+        run("UNTAR", alias: "UNTAR1") {
+            script "modules/nf-core/untar/main.nf"
+            process {
+            """
+            input[0] = Channel.fromList(...)
+            """
+            }
+        }
+
+        run("UNTAR", alias: "UNTAR2") {
+            script "modules/nf-core/untar/main.nf"
+            process {
+            """
+            input[0] = Channel.fromList(...)
+            """
+            }
+        }
+
+        run("UNTAR", alias: "UNTAR3") {
+            script "modules/nf-core/untar/main.nf"
+            process {
+            """
+            input[0] = Channel.fromList(...)
+            """
+            }
+        }
+    }
+
+	test("Test with three different inputs") {
+        when {
+            process {
+                """
+                input[0] = UNTAR1.out.untar.map{ it[1] }
+                input[1] = UNTAR2.out.untar.map{ it[1] }
+                input[2] = UNTAR3.out.untar.map{ it[1] }
+                """
+            }
+        }
+
+        then {
+            ...
+        }
+
+ }
+
+}
+```

src/main/java/com/askimed/nf/test/lang/Dependency.java

@@ -2,16 +2,25 @@
 
 import groovy.lang.Closure;
 
+import java.util.Map;
+
 public class Dependency {
 
 	private String script;
 
 	private String name;
 
+	private String alias;
+
 	private String mapping;
 
-	public Dependency(String name, Closure closure) {
+	public static final String ATTRIBUTE_ALIAS = "alias";
+
+	public Dependency(String name, Map<String, Object> attributes, Closure closure) {
 		this.name = name;
+		if (attributes.containsKey(ATTRIBUTE_ALIAS)) {
+			this.alias = attributes.get(ATTRIBUTE_ALIAS).toString();
+		}
 		closure.setDelegate(this);
 		closure.setResolveStrategy(Closure.DELEGATE_FIRST);
 		closure.call();
@@ -54,6 +63,18 @@ public void setName(String name) {
 		this.name = name;
 	}
 
+	public String getAlias() {
+		return alias;
+	}
+
+	public void setAlias(String alias) {
+		this.alias = alias;
+	}
+
+	public boolean hasAlias() {
+		return alias != null;
+	}
+
 	public String getMapping() {
 		return mapping;
 	}

src/main/java/com/askimed/nf/test/lang/extensions/util/PathConverter.java

@@ -26,6 +26,11 @@ public Object convert(Object value, String key) {
 			if (!path.toFile().exists()) {
 				throw new RuntimeException("Path " + path.toString() + " not found.");
 			}
+		} else if (value instanceof File) {
+			path = ((File) value).toPath();
+			if (!path.toFile().exists()) {
+				throw new RuntimeException("Path " + path.toString() + " not found.");
+			}
 		} else {
 			path = new File(value.toString()).toPath();
 

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

@@ -1,6 +1,8 @@
 package com.askimed.nf.test.lang.process;
 
+import java.util.LinkedHashMap;
 import java.util.List;
+import java.util.Map;
 import java.util.Vector;
 
 import com.askimed.nf.test.core.ITest;
@@ -50,11 +52,15 @@ public void evaluateProcessClosure() {
 
 	}
 
-	public void run(String process, Closure closure) {		
-		Dependency dependency = new Dependency(process, closure);		
+	public void run(Map<String, Object> attributes, String process, Closure closure) {
+		Dependency dependency = new Dependency(process, attributes, closure);
 		dependencies.add(dependency);
 	}
 
+	public void run(String process, Closure closure) {
+		run(new LinkedHashMap<String, Object>(), process, closure);
+	}
+
 	public List<Dependency> getDependencies() {
 		return dependencies;
 	}

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

@@ -1,6 +1,8 @@
 package com.askimed.nf.test.lang.workflow;
 
+import java.util.LinkedHashMap;
 import java.util.List;
+import java.util.Map;
 import java.util.Vector;
 
 import com.askimed.nf.test.core.ITest;
@@ -46,11 +48,15 @@ public void setWorkflow(Workflow workflow) {
 		this.workflow = workflow;
 	}
 
-	public void run(String process, Closure closure) {
-		Dependency dependency = new Dependency(process, closure);
+	public void run(Map<String, Object> attributes, String process, Closure closure) {
+		Dependency dependency = new Dependency(process, attributes, closure);
 		dependencies.add(dependency);
 	}
 
+	public void run(String process, Closure closure) {
+		run(new LinkedHashMap<String, Object>(), process, closure);
+	}
+
 	public List<Dependency> getDependencies() {
 		return dependencies;
 	}

src/main/resources/com/askimed/nf/test/lang/process/WorkflowMock.nf

@@ -8,7 +8,7 @@ params.nf_test_output  = ""
 
 // include dependencies
 <% for (dependency in dependencies) { %>
-include { ${dependency.name} } from '${dependency.script}'
+include { ${dependency.name} ${dependency.hasAlias() ? " as " + dependency.alias : "" } } from '${dependency.script}'
 <% } %>
 
 // include test process
@@ -29,7 +29,7 @@ workflow {
     {
         def input = []
         ${dependency.mapping}
-        ${dependency.name}(*input)
+        ${dependency.hasAlias() ? dependency.alias : dependency.name}(*input)
     }
     <% } %>
 

src/main/resources/com/askimed/nf/test/lang/workflow/WorkflowMock.nf

@@ -8,7 +8,7 @@ params.nf_test_output  = ""
 
 // include dependencies
 <% for (dependency in dependencies) { %>
-include { ${dependency.name} } from '${dependency.script}'
+include { ${dependency.name} ${dependency.hasAlias() ? " as " + dependency.alias : "" } } from '${dependency.script}'
 <% } %>
 
 // include test workflow
@@ -29,7 +29,7 @@ workflow {
     {
         def input = []
         ${dependency.mapping}
-        ${dependency.name}(*input)
+        ${dependency.hasAlias() ? dependency.alias : dependency.name}(*input)
     }
     <% } %>
 

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

@@ -221,9 +221,17 @@ public void testScriptWithRelativePathInSubfolder() throws Exception {
 	public void testDependencies() throws Exception {
 
 		App app = new App();
-		int exitCode = app.run(new String[] { "test", "test-data/process/dependencies/process_data.nf.test" });
+		int exitCode = app.run(new String[] { "test", "test-data/process/dependencies/process_data.nf.test", "--verbose" });
 
-  }
+  	}
+
+	@Test
+	public void testDependenciesWithAlias() throws Exception {
+
+		App app = new App();
+		int exitCode = app.run(new String[] { "test", "test-data/process/dependencies/process_data_alias.nf.test", "--verbose" });
+
+	}
 
   @Test
 	public void testDependenciesAbricate() throws Exception {

test-data/process/dependencies/process_data_alias.nf.test

@@ -0,0 +1,36 @@
+nextflow_process {
+
+    name "Test process data"
+
+    script "./process_data.nf"
+    process "PROCESS_DATA"
+
+    test("Should use process GENERATE_DATA with alias PROCESS_ALIAS to generate input data") {
+
+        setup {
+            run("GENERATE_DATA", alias: "LUKAS") {
+                script "./generate_data.nf"
+                process {
+                    """
+                    input[0] = "nf-core"
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = "lukas"
+                input[1] = LUKAS.out.results
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out.results).match()
+        }
+    }
+
+}