Added nf-test for minia

modules/nf-core/minia/main.nf

@@ -36,4 +36,17 @@ process MINIA {
         minia: \$(echo \$(minia --version 2>&1 | grep Minia) | sed 's/^.*Minia version //;')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.contigs.fa
+    touch ${prefix}.unitigs.fa
+    touch ${prefix}.h5
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        minia: \$(echo \$(minia --version 2>&1 | grep Minia) | sed 's/^.*Minia version //;')
+    END_VERSIONS
+    """
 }

modules/nf-core/minia/meta.yml

@@ -1,7 +1,9 @@
 name: minia
 description: Minia is a short-read assembler based on a de Bruijn graph
 keywords:
-  - assembly
+  - assembler
+  - short-read
+  - de Bruijn
 tools:
   - minia:
       description: |

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

@@ -0,0 +1,71 @@
+
+nextflow_process {
+
+    name "Test Process MINIA"
+    script "../main.nf"
+    process "MINIA"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "minia"
+
+    test("test-minia") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // 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)
+                    ]
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert file(process.out.contigs[0][1]).text.contains('AAA') },
+                { assert file(process.out.unitigs[0][1]).text.contains('CCC') },
+                { assert snapshot(
+                    file(process.out.contigs[0][1]).name,
+                    file(process.out.unitigs[0][1]).name,
+                    file(process.out.h5[0][1]).name,
+                    process.out.versions,
+                    ).match()
+                }
+            )
+        }
+    }
+
+    test("test-minia-stub") {
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // 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)
+                    ]
+				]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}

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

@@ -0,0 +1,82 @@
+{
+    "test-minia": {
+        "content": [
+            "test.contigs.fa",
+            "test.unitigs.fa",
+            "test.h5",
+            [
+                "versions.yml:md5,242f8593f9ee8955fb73580c78f30200"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-05T19:56:44.252673"
+    },
+    "test-minia-stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.contigs.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.unitigs.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.h5:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,242f8593f9ee8955fb73580c78f30200"
+                ],
+                "contigs": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.contigs.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "h5": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.h5:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "unitigs": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.unitigs.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,242f8593f9ee8955fb73580c78f30200"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-09-05T19:52:02.585904"
+    }
+}

tests/config/pytest_modules.yml

@@ -503,9 +503,6 @@ metaphlan3/metaphlan3:
 midas/run:
   - modules/nf-core/midas/run/**
   - tests/modules/nf-core/midas/run/**
-minia:
-  - modules/nf-core/minia/**
-  - tests/modules/nf-core/minia/**
 mitohifi/findmitoreference:
   - modules/nf-core/mitohifi/findmitoreference/**
   - tests/modules/nf-core/mitohifi/findmitoreference/**