Migrate gem2/gemmappability to nf-test

modules/nf-core/gem2/gemmappability/main.nf

@@ -20,8 +20,8 @@ process GEM2_GEMMAPPABILITY {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    def args    = task.ext.args   ?: ''
+    def prefix  = task.ext.prefix ?: "${meta.id}"
     def VERSION = '20200110' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     gem-mappability \\
@@ -38,8 +38,7 @@ process GEM2_GEMMAPPABILITY {
     """
 
     stub:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    def prefix  = task.ext.prefix ?: "${meta.id}"
     def VERSION = '20200110' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
 
     """

modules/nf-core/gem2/gemmappability/tests/main.nf.test

@@ -0,0 +1,70 @@
+nextflow_process {
+
+    name "Test Process GEM2_GEMMAPPABILITY"
+    script "../main.nf"
+    process "GEM2_GEMMAPPABILITY"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "gem2"
+    tag "gem2/gemmappability"
+    tag "gem2/gemindexer"
+
+    setup {
+        run("GEM2_GEMINDEXER") {
+            script "../../gemindexer/main.nf"
+
+            process {
+                """
+                input[0] = [
+                    [id:'test',single_end:false],// meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta',checkIfExists:true)
+                ]
+                """
+            }
+        }
+    }
+
+    test("sarscov2 - fasta") {
+
+        when {
+            process {
+                """
+                input[0] = GEM2_GEMINDEXER.out.index
+                input[1] = "100"
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+
+    test("sarscov2 - fasta -- stub") {
+        options '-stub'
+        when {
+            params {
+                module_args = ''
+            }
+            process {
+                """
+                input[0] = GEM2_GEMINDEXER.out.index
+                input[1] = "100"
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out,
+                    path(process.out.versions[0]).yaml
+                ).match() }
+            )
+        }
+    }
+}

modules/nf-core/gem2/gemmappability/tests/main.nf.test.snap

@@ -0,0 +1,77 @@
+{
+    "sarscov2 - fasta -- stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.mappability:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,a685288af01f7b7a98cb7f042c44f323"
+                ],
+                "map": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.mappability:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,a685288af01f7b7a98cb7f042c44f323"
+                ]
+            },
+            {
+                "GEM2_GEMMAPPABILITY": {
+                    "gem2": 20200110
+                }
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-04-11T15:41:25.596792189"
+    },
+    "sarscov2 - fasta": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.mappability:md5,8380b048fec0e8c4f104f49d2bf784c4"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,a685288af01f7b7a98cb7f042c44f323"
+                ],
+                "map": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.mappability:md5,8380b048fec0e8c4f104f49d2bf784c4"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,a685288af01f7b7a98cb7f042c44f323"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-04-11T15:40:30.596290605"
+    }
+}

tests/config/pytest_modules.yml

@@ -21,9 +21,6 @@ gangstr:
 gatk/indelrealigner:
   - modules/nf-core/gatk/indelrealigner/**
   - tests/modules/nf-core/gatk/indelrealigner/**
-gem2/gemmappability:
-  - modules/nf-core/gem2/gemmappability/**
-  - tests/modules/nf-core/gem2/gemmappability/**
 genescopefk:
   - modules/nf-core/genescopefk/**
   - tests/modules/nf-core/genescopefk/**