Added nf-test for goleft/indexsplit (#6595)

modules/nf-core/goleft/indexsplit/environment.yml

@@ -2,6 +2,5 @@ name: goleft_indexsplit
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::goleft=0.2.4

modules/nf-core/goleft/indexsplit/meta.yml

@@ -13,7 +13,7 @@ tools:
       documentation: "https://github.com/brentp/goleft"
       tool_dev_url: "https://github.com/brentp/goleft"
       doi: "10.1093/gigascience/gix090"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map

modules/nf-core/goleft/indexsplit/tests/main.nf.test

@@ -0,0 +1,68 @@
+
+nextflow_process {
+
+    name "Test Process GOLEFT_INDEXSPLIT"
+    script "../main.nf"
+    process "GOLEFT_INDEXSPLIT"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "goleft"
+    tag "goleft/indexsplit"
+
+    test("test-goleft-indexsplit") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test', single_end:false ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam.bai', checkIfExists: true)
+				]
+				input[1] = [
+				    [ id:'sarscov2'], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+
+				]
+				input[2] = 10
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test-goleft-indexsplit-stub") {
+        options '-stub'
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test', single_end:false ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam.bai', checkIfExists: true)
+				]
+				input[1] = [
+				    [ id:'sarscov2'], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
+				]
+				input[2] = 10
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}

modules/nf-core/goleft/indexsplit/tests/main.nf.test.snap

@@ -0,0 +1,72 @@
+{
+    "test-goleft-indexsplit": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bed:md5,6158ae22773bda2b1380c1f7e324d7a9"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,f71bc54dc512c7e78b0cf5fe7d3f0b05"
+                ],
+                "bed": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bed:md5,6158ae22773bda2b1380c1f7e324d7a9"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,f71bc54dc512c7e78b0cf5fe7d3f0b05"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-06T08:39:21.842028"
+    },
+    "test-goleft-indexsplit-stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,f71bc54dc512c7e78b0cf5fe7d3f0b05"
+                ],
+                "bed": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,f71bc54dc512c7e78b0cf5fe7d3f0b05"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-06T08:39:26.342137"
+    }
+}

tests/config/pytest_modules.yml

@@ -284,9 +284,6 @@ glimpse2/concordance:
 glnexus:
   - modules/nf-core/glnexus/**
   - tests/modules/nf-core/glnexus/**
-goleft/indexsplit:
-  - modules/nf-core/goleft/indexsplit/**
-  - tests/modules/nf-core/goleft/indexsplit/**
 gprofiler2/gost:
   - modules/nf-core/gprofiler2/gost/**
   - tests/modules/nf-core/gprofiler2/gost/**