Added nf-test for mcroni (#6499)

Co-authored-by: Famke Bäuerle <[email protected]>

modules/nf-core/mcroni/main.nf

@@ -40,4 +40,17 @@ process MCRONI {
         mcroni: $VERSION
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '1.0.4' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    """
+    touch ${prefix}.tsv
+    touch ${prefix}.fa
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        mcroni: $VERSION
+    END_VERSIONS
+    """
 }

modules/nf-core/mcroni/meta.yml

@@ -3,13 +3,14 @@ description: Analysis of mcr-1 gene (mobilized colistin resistance) for sequence
 keywords:
   - resistance
   - fasta
+  - mcr-1
 tools:
   - "mcroni":
       description: "Scripts for finding and processing promoter variants upstream of mcr-1"
       homepage: "https://github.com/liampshaw/mcroni"
       documentation: "https://github.com/liampshaw/mcroni"
       tool_dev_url: "https://github.com/liampshaw/mcroni"
-      licence: "['MIT']"
+      licence: ["MIT"]
 input:
   - meta:
       type: map

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

@@ -0,0 +1,57 @@
+
+nextflow_process {
+
+    name "Test Process MCRONI"
+    script "../main.nf"
+    process "MCRONI"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "mcroni"
+
+    test("test-mcroni") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("test-mcroni-stub") {
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}

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

@@ -0,0 +1,96 @@
+{
+    "test-mcroni-stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,0db3954c37fd7f15463e1ca4736a5910"
+                ],
+                "fa": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.fa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "tsv": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,0db3954c37fd7f15463e1ca4736a5910"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-30T21:49:02.89158"
+    },
+    "test-mcroni": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_table.tsv:md5,64f8438dcc476e8b4d762fedc2e3f69e"
+                    ]
+                ],
+                "1": [
+
+                ],
+                "2": [
+                    "versions.yml:md5,0db3954c37fd7f15463e1ca4736a5910"
+                ],
+                "fa": [
+
+                ],
+                "tsv": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_table.tsv:md5,64f8438dcc476e8b4d762fedc2e3f69e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,0db3954c37fd7f15463e1ca4736a5910"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-30T21:48:58.741484"
+    }
+}

tests/config/pytest_modules.yml

@@ -539,9 +539,6 @@ mashtree:
 maxquant/lfq:
   - modules/nf-core/maxquant/lfq/**
   - tests/modules/nf-core/maxquant/lfq/**
-mcroni:
-  - modules/nf-core/mcroni/**
-  - tests/modules/nf-core/mcroni/**
 megan/daa2info:
   - modules/nf-core/megan/daa2info/**
   - tests/modules/nf-core/megan/daa2info/**