Added nf-test for hmtnote/annotate

modules/nf-core/hmtnote/annotate/environment.yml

@@ -4,4 +4,7 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::hmtnote=0.7.2
+  - conda-forge::python=3.6 # Locked with the container
+  - conda-forge::pip=21.3.1
+  - pip:
+      - hmtnote==0.7.2

modules/nf-core/hmtnote/annotate/tests/main.nf.test

@@ -0,0 +1,62 @@
+
+nextflow_process {
+
+    name "Test Process HMTNOTE_ANNOTATE"
+    script "../main.nf"
+    process "HMTNOTE_ANNOTATE"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "hmtnote"
+    tag "hmtnote/annotate"
+
+    test("test-hmtnote-annotate") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true)
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+					path(process.out.vcf[0][1]).vcf.variantsMD5,
+					process.out.versions
+					).match()
+				}
+            )
+        }
+    }
+
+    test("test-hmtnote-annotate-stub") {
+        options '-stub'
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true)
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}

modules/nf-core/hmtnote/annotate/tests/main.nf.test.snap

@@ -0,0 +1,48 @@
+{
+    "test-hmtnote-annotate": {
+        "content": [
+            "98d1056442ec88659f26dfb1251b6f74",
+            [
+                "versions.yml:md5,8ee58af72515ea6d362a7721c3ba1340"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-02T13:58:45.987177"
+    },
+    "test-hmtnote-annotate-stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_annotated.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,8ee58af72515ea6d362a7721c3ba1340"
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_annotated.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,8ee58af72515ea6d362a7721c3ba1340"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-02T13:58:54.748392"
+    }
+}

modules/nf-core/hmtnote/annotate/tests/nextflow.config

@@ -0,0 +1,5 @@
+process {
+    withName: HMTNOTE_ANNOTATE {
+        ext.args = '--basic --variab'
+    }
+}

tests/config/pytest_modules.yml

@@ -185,9 +185,6 @@ hmmer/eslalimask:
 hmmer/eslreformat:
   - modules/nf-core/hmmer/eslreformat/**
   - tests/modules/nf-core/hmmer/eslreformat/**
-hmtnote/annotate:
-  - modules/nf-core/hmtnote/annotate/**
-  - tests/modules/nf-core/hmtnote/annotate/**
 icountmini/metagene:
   - modules/nf-core/icountmini/metagene/**
   - tests/modules/nf-core/icountmini/metagene/**