Added nf-test for vt/decompose (#6241)

modules/nf-core/vt/decompose/meta.yml

@@ -13,7 +13,7 @@ tools:
       homepage: "https://genome.sph.umich.edu/wiki/Vt"
       documentation: "https://genome.sph.umich.edu/wiki/Vt"
       tool_dev_url: "https://github.com/atks/vt"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map

modules/nf-core/vt/decompose/tests/main.nf.test

@@ -0,0 +1,60 @@
+
+nextflow_process {
+
+    name "Test Process VT_DECOMPOSE"
+    script "../main.nf"
+    process "VT_DECOMPOSE"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "vt"
+    tag "vt/decompose"
+
+    test("test-vt-decompose") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				[ id:'test', single_end:false ], // meta map
+				file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+				[]
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test-vt-decompose-intervals") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				[ id:'test', single_end:false ], // meta map
+				file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true),
+				file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}

modules/nf-core/vt/decompose/tests/main.nf.test.snap

@@ -0,0 +1,72 @@
+{
+    "test-vt-decompose-intervals": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "decompose.vcf.gz:md5,892b6b5c55c69afd3a96cd9bfd8ab743"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,f10f0ae7e4b74341393c2a9fc87afa87"
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "decompose.vcf.gz:md5,892b6b5c55c69afd3a96cd9bfd8ab743"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,f10f0ae7e4b74341393c2a9fc87afa87"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-22T17:30:33.250927"
+    },
+    "test-vt-decompose": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "decompose.vcf.gz:md5,892b6b5c55c69afd3a96cd9bfd8ab743"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,f10f0ae7e4b74341393c2a9fc87afa87"
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "decompose.vcf.gz:md5,892b6b5c55c69afd3a96cd9bfd8ab743"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,f10f0ae7e4b74341393c2a9fc87afa87"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-22T17:30:27.223776"
+    }
+}

modules/nf-core/vt/decompose/tests/nextflow.config

@@ -0,0 +1,5 @@
+process {
+    withName: VT_DECOMPOSE {
+        ext.prefix = "decompose"
+    }
+}

tests/config/pytest_modules.yml

@@ -1668,9 +1668,6 @@ vsearch/sintax:
 vsearch/usearchglobal:
   - modules/nf-core/vsearch/usearchglobal/**
   - tests/modules/nf-core/vsearch/usearchglobal/**
-vt/decompose:
-  - modules/nf-core/vt/decompose/**
-  - tests/modules/nf-core/vt/decompose/**
 vt/normalize:
   - modules/nf-core/vt/normalize/**
   - tests/modules/nf-core/vt/normalize/**