Merge pull request #2586 from mashehu/add-stubs-test-template

add stub test to modules template
nf-core · Dec 19, 2023 · 2622557 · 2622557
2 parents d65d9cf + 5774a5a
commit 2622557
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diff --git a/nf_core/module-template/tests/main.nf.test b/nf_core/module-template/tests/main.nf.test
@@ -37,6 +37,38 @@ nextflow_process {
             }
         }
 
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+                //TODO nf-core: Add all required assertions to verify the test output.
+                // See https://nf-co.re/docs/contributing/tutorials/nf-test_assertions for more information and examples.
+            )
+        }
+
+    }
+
+    // TODO nf-core: Change the test name preferably indicating the test-data and file-format used but keep the " - stub" suffix.
+    test("sarscov2 - bam - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                // TODO nf-core: define inputs of the process here. Example:
+                {% if has_meta %}
+                input = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+                    ]
+                {%- else %}
+                input = file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true)
+                {%- endif %}
+                """
+            }
+        }
+
         then {
             assertAll(
                 { assert process.success },

diff --git a/nf_core/subworkflow-template/tests/main.nf.test b/nf_core/subworkflow-template/tests/main.nf.test
@@ -2,7 +2,7 @@
 // nf-core subworkflows test {{ component_name }}
 nextflow_workflow {
 
-    name "Test Workflow {{ component_name_underscore|upper }}"
+    name "Test Subworkflow {{ component_name_underscore|upper }}"
     script "../main.nf"
     workflow "{{ component_name_underscore|upper }}"