Added nf-test for ngmerge (#6269)

* Added nf-test for ngmerge

* Fixed assertion

modules/nf-core/ngmerge/meta.yml

@@ -12,7 +12,7 @@ tools:
       documentation: "https://github.com/jsh58/NGmerge"
       tool_dev_url: "https://github.com/jsh58/NGmerge"
       doi: "10.1186/s12859-018-2579-2"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map

modules/nf-core/ngmerge/tests/main.nf.test

@@ -0,0 +1,43 @@
+
+nextflow_process {
+
+    name "Test Process NGMERGE"
+    script "../main.nf"
+    process "NGMERGE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "ngmerge"
+
+    test("test-ngmerge") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test', single_end:false ], // meta map
+				    [
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true),
+				        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)
+                    ]
+				]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.merged_reads[0][1]).linesGzip[0].contains('ERR5069949') },
+                { assert snapshot(
+					file(process.out.merged_reads[0][1]).name,
+					file(process.out.unstitched_read1[0][1]).name,
+					file(process.out.unstitched_read2[0][1]).name,
+					process.out.versions
+					).match()
+				}
+            )
+        }
+    }
+
+}

modules/nf-core/ngmerge/tests/main.nf.test.snap

@@ -0,0 +1,17 @@
+{
+    "test-ngmerge": {
+        "content": [
+            "test.merged.fq.gz",
+            "test_unstitched_1.fastq.gz",
+            "test_unstitched_2.fastq.gz",
+            [
+                "versions.yml:md5,fbe3b4187e1c70c016f738aeff8ab5f1"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-23T12:02:38.100015"
+    }
+}

tests/config/pytest_modules.yml

@@ -983,9 +983,6 @@ nextgenmap:
 ngmaster:
   - modules/nf-core/ngmaster/**
   - tests/modules/nf-core/ngmaster/**
-ngmerge:
-  - modules/nf-core/ngmerge/**
-  - tests/modules/nf-core/ngmerge/**
 nucmer:
   - modules/nf-core/nucmer/**
   - tests/modules/nf-core/nucmer/**