Update to topic magus/guidetree (#12132)

* Update to topic

* Apply suggestion from @LouisLeNezet

* Update meta

Author: LouisLeNezet

modules/nf-core/magus/guidetree/main.nf

@@ -12,7 +12,7 @@ process MAGUS_GUIDETREE {
 
     output:
     tuple val(meta), path("*.tree"), emit: tree
-    path "versions.yml"            , emit: versions
+    tuple val("${task.process}"), val('magus'), eval('magus --version'), emit: versions_magus, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -22,26 +22,16 @@ process MAGUS_GUIDETREE {
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     magus \\
-        -np $task.cpus \\
-        -i $fasta \\
+        -np ${task.cpus} \\
+        -i ${fasta} \\
         -o ${prefix}.tree \\
         --onlyguidetree TRUE \\
-        $args
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        MAGUS: \$(magus --version)
-    END_VERSIONS
+        ${args}
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.tree
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        MAGUS: \$(magus --version)
-    END_VERSIONS
     """
 }

modules/nf-core/magus/guidetree/meta.yml

@@ -1,4 +1,3 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
 name: "magus_guidetree"
 description: Multiple Sequence Alignment using Graph Clustering
 keywords:
@@ -13,7 +12,8 @@ tools:
       documentation: "https://github.com/vlasmirnov/MAGUS"
       tool_dev_url: "https://github.com/vlasmirnov/MAGUS"
       doi: "10.1093/bioinformatics/btaa992"
-      licence: ["MIT"]
+      licence:
+        - "MIT"
       identifier: biotools:magus
 
 input:
@@ -42,12 +42,28 @@ output:
           pattern: "*.tree"
           ontologies:
             - edam: http://edamontology.org/format_2006 # PHYLOGENETIC TREE
+  versions_magus:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - magus:
+          type: string
+          description: The name of the tool
+      - magus --version:
+          type: eval
+          description: The expression to obtain the version of the tool
+
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - magus:
+          type: string
+          description: The name of the tool
+      - magus --version:
+          type: eval
+          description: The expression to obtain the version of the tool
+
 authors:
   - "@lrauschning"

modules/nf-core/magus/guidetree/tests/main.nf.test

@@ -14,9 +14,10 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = [ [ id:'test' ], // meta map
-                             file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true)
-                           ]
+                input[0] = [
+                    [ id:'test' ],
+                    file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true)
+                ]
                 """
             }
         }
@@ -32,7 +33,28 @@ nextflow_process {
                 { assert path(process.out.tree[0][1]).getText().contains("1atx") },
                 { assert path(process.out.tree[0][1]).getText().contains("1sh1") },
                 { assert path(process.out.tree[0][1]).getText().contains("1bds") },
-                { assert snapshot(process.out.versions).match("versions") }
+                { assert snapshot(sanitizeOutput(process.out, unstableKeys:["tree"])).match() }
+            )
+        }
+    }
+
+    test("setoxin - fasta -- stub") {
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
     }

modules/nf-core/magus/guidetree/tests/main.nf.test.snap

@@ -1,23 +1,54 @@
 {
-    "versions": {
+    "setoxin - fasta": {
         "content": [
-            [
-                "versions.yml:md5,5a2ad92c9ea945c4bf4890f02ca2562f"
-            ]
+            {
+                "tree": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.tree"
+                    ]
+                ],
+                "versions_magus": [
+                    [
+                        "MAGUS_GUIDETREE",
+                        "magus",
+                        "0.2.0"
+                    ]
+                ]
+            }
         ],
-        "timestamp": "2024-03-28T18:25:41.292337485"
+        "timestamp": "2026-06-22T22:01:53.406955105",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.3"
+        }
     },
-    "tree": {
+    "setoxin - fasta -- stub": {
         "content": [
-            [
-                [
-                    {
-                        "id": "test"
-                    },
-                    "test.tree:md5,c742636229d166322a2824d409595738"
+            {
+                "tree": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.tree:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions_magus": [
+                    [
+                        "MAGUS_GUIDETREE",
+                        "magus",
+                        "0.2.0"
+                    ]
                 ]
-            ]
+            }
         ],
-        "timestamp": "2024-03-28T18:25:41.226027114"
+        "timestamp": "2026-06-22T21:48:03.41595829",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.3"
+        }
     }
 }