Added nf-test for haplogrep2/classify (#6572)

nf-core · Sep 5, 2024 · dab11bf · dab11bf
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commit dab11bf
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Showing 7 changed files with 135 additions and 43 deletions.
diff --git a/modules/nf-core/haplogrep2/classify/meta.yml b/modules/nf-core/haplogrep2/classify/meta.yml
@@ -1,14 +1,16 @@
 name: "haplogrep2_classify"
 description: classification into haplogroups
 keywords:
-  - haplogroups.
+  - haplogroups
+  - classify
+  - mtDNA
 tools:
   - "haplogrep2":
       description: "A tool for mtDNA haplogroup classification."
       homepage: "https://github.com/seppinho/haplogrep-cmd"
       documentation: "https://github.com/seppinho/haplogrep-cmd"
       tool_dev_url: "https://github.com/seppinho/haplogrep-cmd"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map

diff --git a/modules/nf-core/haplogrep2/classify/tests/main.nf.test b/modules/nf-core/haplogrep2/classify/tests/main.nf.test
@@ -0,0 +1,59 @@
+
+nextflow_process {
+
+    name "Test Process HAPLOGREP2_CLASSIFY"
+    script "../main.nf"
+    process "HAPLOGREP2_CLASSIFY"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "haplogrep2"
+    tag "haplogrep2/classify"
+
+    test("test-haplogrep2-classify") {
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test', single_end:false ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_chrM.vcf.gz', checkIfExists: true)
+				]
+				input[1] = 'vcf'
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test-haplogrep2-classify-stub") {
+        options '-stub'
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test', single_end:false ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_chrM.vcf.gz', checkIfExists: true)
+				]
+				input[1] = 'vcf'
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/haplogrep2/classify/tests/main.nf.test.snap b/modules/nf-core/haplogrep2/classify/tests/main.nf.test.snap
@@ -0,0 +1,72 @@
+{
+    "test-haplogrep2-classify": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.txt:md5,cf9a4cf886e75233083313d8758566a0"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,b89c2ae3ff8722a536c4042ed4330f25"
+                ],
+                "txt": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.txt:md5,cf9a4cf886e75233083313d8758566a0"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,b89c2ae3ff8722a536c4042ed4330f25"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-05T21:15:54.953862"
+    },
+    "test-haplogrep2-classify-stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,b89c2ae3ff8722a536c4042ed4330f25"
+                ],
+                "txt": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,b89c2ae3ff8722a536c4042ed4330f25"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-05T21:12:30.597805"
+    }
+}
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -335,9 +335,6 @@ gunc/run:
 hapibd:
   - modules/nf-core/hapibd/**
   - tests/modules/nf-core/hapibd/**
-haplogrep2/classify:
-  - modules/nf-core/haplogrep2/classify/**
-  - tests/modules/nf-core/haplogrep2/classify/**
 hicexplorer/hicpca:
   - modules/nf-core/hicexplorer/hicpca/**
   - tests/modules/nf-core/hicexplorer/hicpca/**

diff --git a/tests/modules/nf-core/haplogrep2/classify/main.nf b/tests/modules/nf-core/haplogrep2/classify/main.nf
diff --git a/tests/modules/nf-core/haplogrep2/classify/nextflow.config b/tests/modules/nf-core/haplogrep2/classify/nextflow.config
diff --git a/tests/modules/nf-core/haplogrep2/classify/test.yml b/tests/modules/nf-core/haplogrep2/classify/test.yml