Added nf-test for hypo (#6571)

* Added nf-test for hypo

* Removed defaults

modules/nf-core/hypo/environment.yml

@@ -2,6 +2,5 @@ name: hypo
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - bioconda::hypo=1.0.3

modules/nf-core/hypo/meta.yml

@@ -12,7 +12,7 @@ tools:
       documentation: "https://github.com/kensung-lab/hypo/blob/master/README.md"
       tool_dev_url: "https://github.com/kensung-lab/hypo"
       doi: "10.1101/2019.12.19.882506"
-      licence: "['GPL v3']"
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map

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

@@ -0,0 +1,76 @@
+
+nextflow_process {
+
+    name "Test Process HYPO"
+    script "../main.nf"
+    process "HYPO"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "hypo"
+
+    test("test-hypo") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test', single_end:false ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true)
+				]
+				input[1] = [
+				    [ 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)
+				    ]
+				]
+				input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+				input[3] = 29903
+				input[4] = 5
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test-hypo-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.paired_end.bam', checkIfExists: true)
+				]
+				input[1] = [
+				    [ 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)
+				    ]
+				]
+				input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+				input[3] = 29903
+				input[4] = 5
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}

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

@@ -0,0 +1,72 @@
+{
+    "test-hypo-stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,9529d9976a97d2d8e2d1cc00035906c9"
+                ],
+                "fasta": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fasta:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,9529d9976a97d2d8e2d1cc00035906c9"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-05T21:15:49.822312"
+    },
+    "test-hypo": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fasta:md5,d326ff4fc91e25617c43d678f68187ad"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,9529d9976a97d2d8e2d1cc00035906c9"
+                ],
+                "fasta": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fasta:md5,d326ff4fc91e25617c43d678f68187ad"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,9529d9976a97d2d8e2d1cc00035906c9"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-05T21:15:37.149543"
+    }
+}

tests/config/pytest_modules.yml

@@ -353,9 +353,6 @@ hmtnote/annotate:
 homer/makeucscfile:
   - modules/nf-core/homer/makeucscfile/**
   - tests/modules/nf-core/homer/makeucscfile/**
-hypo:
-  - modules/nf-core/hypo/**
-  - tests/modules/nf-core/hypo/**
 icountmini/metagene:
   - modules/nf-core/icountmini/metagene/**
   - tests/modules/nf-core/icountmini/metagene/**