Add $launchDir and change directory where Nextflow processes are executed

docs/docs/assertions/assertions.md

@@ -38,11 +38,6 @@ process.out.outputCh = [
 ]
 ``` 
 
-`nf-test` cannot guarantee the order of nextflow channels that contain alternative object types, such as maps. A warning message appears in the console in such cases to highlight the potential issue. To test these channels, the `contains` and `assertContainsInAnyOrder` methods described below can be used
-```
-Warning: Cannot sort channel, order not deterministic. Unsupported objects types:
-```
-
 ## Using `with`
 
 This assertions...

docs/docs/testcases/global_variables.md

@@ -1,80 +1,57 @@
-# Params and Global Variables
+# Global Variables
 
-## Params
+The following variables are available and can be used in `setup`, `when`, `then` and `cleanup` closures.
 
-The `params` block is optional and is a simple map that can be used to overwrite Nextflow's input `params`. The `params` block is located in the `when` block of a testcase. You can set params manually:
+|Name|Description| Example |
+|---|---|---|
+|`baseDir` or<br/>`projectDir`| The directory where the `nf-test.config` script is located. | `mypipeline`|
+|`moduleDir`| The directory where the module script is located  | `mypipeline/modules/mymodule` |
+|`moduleTestDir`| The directory where the test script is located  | `mypipeline/tests/modules/mymodule` |
+|`launchDir`| The directory where the test is run. | `mypipeline/.nf-test/tests/<test_hash>` |
+|`metaDir`| The directory where all meta are located (e.g. `mock.nf`).| `mypipeline/.nf-test/tests/<test_hash>/meta` |
+|`workDir`| The directory where tasks temporary files are created.| `mypipeline/.nf-test/tests/<test_hash>/work` |
+|`outputDir`| An output directory in the `$launchDir` that can be used to store output files. The variable contains the absolute path. If you need a relative outpu directory see [`launchDir` example](#launchdir). | `mypipeline/.nf-test/tests/<test_hash>/output` |
+|`params`| Dictionary like object holding all parameters. | |
 
-```Groovy
-when {
-    params {
-        outdir = "output"
-    }
-}
-```
-
-It is also possible to set nested params using the same syntax as in your Nextflow script:
+## Examples
 
-```Groovy
-when {
-    params {
-        output {
-          dir = "output"
-        }
-    }
-}
-```
+### `outputDir`
 
-In addition, you can load the `params` from a JSON file:
+This variable points to the directory within the temporary test directory (`.nf-test/tests/<test-dir>/output/`). The variable can be set under params:
 
 ```Groovy
-when {
-    params {
-        load("$baseDir/tests/params.json")
-    }
+params {
+    outdir = "$outputDir"
 }
 ```
 
-or from a YAML file:
+### `baseDir`
+
+This variable points to the directory to locate the base directory of the main nf-test config. The variable can be used e.g. in the process definition to build absolute paths for input files:
 
 ```Groovy
-when {
-    params {
-        load("$baseDir/tests/params.yaml")
-    }
+process {
+    """
+    file1 = file("$baseDir/tests/input/file123.gz")
+    """
 }
 ```
 
-nf-test allows to combine both techniques and therefor it is possible to overwrite one or more `params` from the json file:
+### `launchDir`
+
+This variable points to the directory where the test is executed. This can be used get access to results that are created in an relative output directory:
 
 ```Groovy
 when {
     params {
-        load("$baseDir/tests/params.json")
-        outputDir = "new/output/path"
+        outdir = "results"
     }
 }
 ```
 
-## Global Variables
-
-### `outputDir`
-
-This variable points to the directory within the temporary test directory (`.nf-test/tests/<test-dir>/output/`). The variable can be set under params:
-
 ```Groovy
-params {
-    outdir = "$outputDir"
+then {
+    assert path("$launchDir/results").exists()
 }
-```
-
-### `baseDir`
 
-This variable points to the directory to locate the base directory of the main nf-test config. The variable can be used e.g. in the process definition to build absolute paths for input files:
-
-```Groovy
-process {
-    """
-    file1 = file("$baseDir/tests/input/file123.gz")
-    """
-}
-```
+```

docs/docs/testcases/nextflow_process.md

@@ -66,7 +66,7 @@ assert process.out[0].size() == 3
 
 // first element is "hello"
 assert process.out[0].get(0) == "hello"
-````
+```
 
 ## Example
 

docs/docs/testcases/params.md

@@ -0,0 +1,64 @@
+# Params Dictionary
+
+The `params` block is optional and is a simple map that can be used to overwrite Nextflow's input `params`. The `params` block is located in the `when` block of a testcase. You can set params manually:
+
+```Groovy
+when {
+    params {
+        outdir = "output"
+    }
+}
+```
+
+It is also possible to set nested params using the same syntax as in your Nextflow script:
+
+```Groovy
+when {
+    params {
+        output {
+          dir = "output"
+        }
+    }
+}
+```
+
+The `params` map can also be used in the `then` block:
+
+```Groovy
+then {
+    assert params.output == "output"    
+}
+```
+
+## Load params from files
+
+In addition, you can load the `params` from a JSON file:
+
+```Groovy
+when {
+    params {
+        load("$baseDir/tests/params.json")
+    }
+}
+```
+
+or from a YAML file:
+
+```Groovy
+when {
+    params {
+        load("$baseDir/tests/params.yaml")
+    }
+}
+```
+
+nf-test allows to combine both techniques and therefor it is possible to overwrite one or more `params` from the json file:
+
+```Groovy
+when {
+    params {
+        load("$baseDir/tests/params.json")
+        outputDir = "new/output/path"
+    }
+}
+```

example/hello.nf.test

@@ -5,8 +5,14 @@ nextflow_pipeline {
 
   test("hello world example should start 4 processes") {
     expect {
-      assert workflow.success
-      assert snapshot(workflow).match()
+      with(workflow) {
+        assert success
+        assert trace.tasks().size() == 4
+        assert "Ciao world!" in stdout
+        assert "Bonjour world!" in stdout
+        assert "Hello world!" in stdout
+        assert "Hola world!" in stdout
+      }
     }
   }
 

mkdocs.yml

@@ -42,7 +42,8 @@ nav:
       - Workflow Testing: docs/testcases/nextflow_workflow.md
       - Process Testing: docs/testcases/nextflow_process.md
       - Function Testing: docs/testcases/nextflow_function.md
-      - Params and Global Variables: docs/testcases/global_variables.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
@@ -51,7 +52,7 @@ nav:
       - 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):
+    - Command Line Interface (CLI):
       - init: docs/cli/init.md
       - generate: docs/cli/generate.md
       - test: docs/cli/test.md

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

@@ -82,7 +82,6 @@ public Integer execute() throws Exception {
 
 			String defaultProfile = null;
 			File defaultConfigFile = null;
-			File workDir = new File(".nf-test");
 			String libDir = lib;
 			boolean defaultWithTrace = true;
 			try {
@@ -94,7 +93,6 @@ public Integer execute() throws Exception {
 					defaultProfile = config.getProfile();
 					defaultConfigFile = config.getConfigFile();
 					defaultWithTrace = config.isWithTrace();
-					workDir = new File(config.getWorkDir());
 					if (!libDir.isEmpty()) {
 						libDir += ":";
 					}
@@ -151,7 +149,6 @@ public Integer execute() throws Exception {
 			engine.setScripts(scripts);
 			engine.setTagQuery(tagQuery);
 			engine.setDebug(debug);
-			engine.setWorkDir(workDir);
 			engine.setUpdateSnapshot(updateSnapshot);
 			engine.setCleanSnapshot(cleanSnapshot);
 			engine.setLibDir(libDir);

src/main/java/com/askimed/nf/test/config/Config.java

@@ -16,6 +16,8 @@ public class Config {
 
 	public static final String DEFAULT_NEXTFLOW_CONFIG = "tests/nextflow.config";
 
+	public static final String DEFAULT_HOME = ".nf-test";
+
 	private String workDir = ".nf-test";
 
 	private String testsDir = "tests";