stub and nf-test created for raxmlng

modules/nf-core/raxmlng/main.nf

@@ -7,28 +7,51 @@ process RAXMLNG {
         'biocontainers/raxml-ng:1.0.3--h32fcf60_0' }"
 
     input:
-    path alignment
+    tuple val(meta), path(alignment), val(model)
 
     output:
-    path "*.raxml.bestTree", emit: phylogeny
-    path "*.raxml.support" , optional:true, emit: phylogeny_bootstrapped
-    path "versions.yml"    , emit: versions
+    tuple val(meta), path("*.raxml.bestTree")              , emit: phylogeny
+    tuple val(meta), path("*.raxml.support"), optional:true, emit: phylogeny_bootstrapped
+    path "versions.yml"                                    , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
     """
     raxml-ng \\
         $args \\
         --msa $alignment \\
+        --model $model \\
         --threads $task.cpus \\
-        --prefix output
+        --prefix ${prefix}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         raxmlng: \$(echo \$(raxml-ng --version 2>&1) | sed 's/^.*RAxML-NG v. //; s/released.*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def args = task.ext.args ?: params.raxmlng_args ?: ''
+    def prefix = task.ext.prefix ?: meta.id
+    if (!meta.id) {
+        error "Input meta map does not contain 'id'. Received: ${meta}"
+    }
+    // Use a dedicated param for stub testing the bootstrap output scenario
+    def touch_support = args.contains('--bootstrap') || args.contains('--bs-trees') ? "touch ${prefix}.raxml.support" : ""
+    """
+    # Create stub output files
+    touch ${prefix}.raxml.bestTree
+    ${touch_support}
+
+    # Create versions.yml
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        raxmlng: stub_version
+    END_VERSIONS
+    """
 }

modules/nf-core/raxmlng/meta.yml

@@ -13,24 +13,41 @@ tools:
       documentation: https://github.com/amkozlov/raxml-ng/wiki
       tool_dev_url: https://github.com/amkozlov/raxml-ng
       doi: 10.1093/bioinformatics/btz305
-      licence: ["GPL v2-or-later"]
+      license: ["GPL v2-or-later"]
       identifier: ""
 input:
-  - - alignment:
+  - - meta:
+        type: map
+        description: Groovy Map containing sample information (e.g. [ id:'sample1' ])
+    - alignment:
         type: file
         description: A FASTA format multiple sequence alignment file
         pattern: "*.{fasta,fas,fa,mfa}"
+    - model:
+        type: string
+        description: The substitution model to use for the phylogenetic inference
+
 output:
   - phylogeny:
+      - meta:
+          type: map
+          description: Groovy Map containing sample information
+          pattern: "*.{raxml.bestTree}"
       - "*.raxml.bestTree":
-          type: file
-          description: A phylogeny in Newick format
+          type: map
+          description: Groovy Map containing sample information
           pattern: "*.{raxml.bestTree}"
   - phylogeny_bootstrapped:
+      - meta:
+          type: map
+          description: Groovy Map containing sample information
+          pattern: "*.{raxml.support}"
+          optional: true
       - "*.raxml.support":
-          type: file
-          description: A phylogeny in Newick format with bootstrap values
+          type: map
+          description: Groovy Map containing sample information
           pattern: "*.{raxml.support}"
+          optional: true
   - versions:
       - versions.yml:
           type: file

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

@@ -0,0 +1,93 @@
+nextflow_process {
+    name "Test Process RAXMLNG"
+    script "../main.nf"
+    process "RAXMLNG"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "raxmlng"
+
+    test("raxmlng - main") {
+        when {
+            process {
+                """
+                // alignment fasta file is required
+                input[0] = [
+                [ id:'test' ], // meta map with id
+                file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/informative_sites.fas', checkIfExists: true), // alignment fasta
+                'GTR+G' // model
+                ]
+                """
+            }
+
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                // Check phylogeny output (tuple: meta, path)
+                { assert process.out.phylogeny.size() == 1 },
+                { assert process.out.phylogeny[0][0].id == 'test' }, // Check meta.id passed through
+                { assert process.out.phylogeny[0][1].toString().endsWith(".raxml.bestTree") },
+                { assert process.out.phylogeny[0][1].toString().contains("test") }, // Check if prefix 'test' was used
+                // Check optional bootstrapped output (should be empty)
+                { assert process.out.phylogeny_bootstrapped.isEmpty() },
+                // Check versions
+                { assert process.out.versions.size() == 1 },
+                { assert process.out.versions[0].toString().endsWith("versions.yml") },
+                { assert snapshot(process.out.versions[0]).match("versions_yml") } // Snapshot specific file
+            )
+        }
+    }
+
+
+    test("raxmlng - stub - no bootstrap") {
+    options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                            [ id:'test_stub' ], // meta map
+                            file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/informative_sites.fas', checkIfExists: true), // alignment file path
+                            'GTR+G' // model string
+                        ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                // This will show phylogeny and versions, but not phylogeny_bootstrapped
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+
+        test("raxmlng - stub - with bootstrap") {
+        options "-stub"
+        when {
+            params.test_stub_bootstrap = true
+            params {
+            // Set the bootstrap parameter to true
+            test_stub_bootstrap = true
+            }
+            process {
+            """
+            input[0] = [
+                [ id:'test_bootstrap' ], // meta map
+                file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/informative_sites.fas', checkIfExists: true), // alignment file path
+                'GTR+G' // model string
+            ]
+            """
+            }
+        }
+        then {
+            assertAll (
+            { assert process.success },
+            { assert snapshot(process.out).match("stub_with_bootstrap") }
+            )
+        }
+    }
+}

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

@@ -0,0 +1,100 @@
+{
+    "versions_yml": {
+        "content": [
+            "versions.yml:md5,e5a855c4c9bcde2084ec9e34861379f0"
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-03-31T17:18:00.904972153"
+    },
+    "stub_with_bootstrap": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_bootstrap"
+                        },
+                        "test_bootstrap.raxml.bestTree:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test_bootstrap"
+                        },
+                        "test_bootstrap.raxml.support:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,e7caecc35f1746920b7e0991adc59b4c"
+                ],
+                "phylogeny": [
+                    [
+                        {
+                            "id": "test_bootstrap"
+                        },
+                        "test_bootstrap.raxml.bestTree:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "phylogeny_bootstrapped": [
+                    [
+                        {
+                            "id": "test_bootstrap"
+                        },
+                        "test_bootstrap.raxml.support:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,e7caecc35f1746920b7e0991adc59b4c"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-03-31T17:55:18.655533044"
+    },
+    "stub_no_bootstrap": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_stub"
+                        },
+                        "test_stub.raxml.bestTree:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+
+                ],
+                "2": [
+                    "versions.yml:md5,e7caecc35f1746920b7e0991adc59b4c"
+                ],
+                "phylogeny": [
+                    [
+                        {
+                            "id": "test_stub"
+                        },
+                        "test_stub.raxml.bestTree:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "phylogeny_bootstrapped": [
+
+                ],
+                "versions": [
+                    "versions.yml:md5,e7caecc35f1746920b7e0991adc59b4c"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.5"
+        },
+        "timestamp": "2025-03-31T17:55:15.617725178"
+    }
+}

tests/config/pytest_modules.yml

@@ -184,15 +184,9 @@ purgedups/purgedups:
 pydamage/filter:
   - modules/nf-core/pydamage/filter/**
   - tests/modules/nf-core/pydamage/filter/**
-raxmlng:
-  - modules/nf-core/raxmlng/**
-  - tests/modules/nf-core/raxmlng/**
 rhocall/annotate:
   - modules/nf-core/rhocall/annotate/**
   - tests/modules/nf-core/rhocall/annotate/**
-roary:
-  - modules/nf-core/roary/**
-  - tests/modules/nf-core/roary/**
 scramble/clusteranalysis:
   - modules/nf-core/scramble/clusteranalysis/**
   - tests/modules/nf-core/scramble/clusteranalysis/**