Swap samtools dict to nftest

modules/nf-core/samtools/dict/tests/main.nf.test

@@ -0,0 +1,59 @@
+nextflow_process {
+
+    name "Test Process SAMTOOLS_DICT"
+    script "../main.nf"
+    process "SAMTOOLS_DICT"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "samtools"
+    tag "samtools/dict"
+
+    test("sarscov2 - fasta") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match() },
+                { assert path(process.out.dict[0][1]).readLines().first().contains("@HD\tVN:1.0\tSO:unsorted") }
+            )
+        }
+
+    }
+
+    test("sarscov2 - fasta - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}

modules/nf-core/samtools/dict/tests/main.nf.test.snap

@@ -0,0 +1,49 @@
+{
+    "sarscov2 - fasta - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "genome.fasta.dict:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,47f9e889ed1e779cb54e61d707a7135d"
+                ],
+                "dict": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "genome.fasta.dict:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,47f9e889ed1e779cb54e61d707a7135d"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-18T09:43:30.509703257"
+    },
+    "sarscov2 - fasta": {
+        "content": [
+            [
+                "versions.yml:md5,0af6b2d2d6d9d96bc5abe98b99b91446"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.3"
+        },
+        "timestamp": "2024-07-18T09:51:18.221597999"
+    }
+}

tests/config/pytest_modules.yml

@@ -1346,9 +1346,6 @@ samtools/collatefastq:
 samtools/depth:
   - modules/nf-core/samtools/depth/**
   - tests/modules/nf-core/samtools/depth/**
-samtools/dict:
-  - modules/nf-core/samtools/dict/**
-  - tests/modules/nf-core/samtools/dict/**
 samtools/fasta:
   - modules/nf-core/samtools/fasta/**
   - tests/modules/nf-core/samtools/fasta/**