Migrate annosine to topic channels

modules/nf-core/annosine/main.nf

@@ -15,15 +15,14 @@ process ANNOSINE {
     output:
     tuple val(meta), path("${prefix}.log"), emit: log
     tuple val(meta), path("${prefix}.fa") , emit: fa, optional: true
-    path "versions.yml"                   , emit: versions
+    tuple val("${task.process}"), val('annosine'), eval('pip show annosine2 | grep "^Version" | sed "s/Version: //"'), emit: versions_annosine, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args    = task.ext.args   ?: ''
     prefix      = task.ext.prefix ?: "${meta.id}_annosine"
-    def VERSION = '2.0.8' // WARN: Manually update when changing Bioconda assets
     if ( "${fasta}" == "${prefix}.fa" ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     """
     AnnoSINE_v2 \\
@@ -38,24 +37,13 @@ process ANNOSINE {
         ${prefix}/Seed_SINE.fa \\
         ${prefix}.fa \\
         || echo 'AnnoSINE_v2 did not find SINE sequences. See log for details!'
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        annosine: ${VERSION}
-    END_VERSIONS
     """
 
     stub:
     prefix      = task.ext.prefix ?: "${meta.id}_annosine"
-    def VERSION = '2.0.8' // WARN: Manually update when changing Bioconda assets
     if ( "${fasta}" == "${prefix}.fa" ) error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     """
     touch ${prefix}.log
     touch ${prefix}.fa
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        annosine: ${VERSION}
-    END_VERSIONS
     """
 }

modules/nf-core/annosine/meta.yml

@@ -1,4 +1,3 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
 name: "annosine"
 description: Accelerating de novo SINE annotation in plant and animal genomes
 keywords:
@@ -13,9 +12,9 @@ tools:
       documentation: "https://github.com/liaoherui/AnnoSINE_v2"
       tool_dev_url: "https://github.com/liaoherui/AnnoSINE_v2"
       doi: "10.1101/2024.03.01.582874"
-      licence: ["MIT"]
+      licence:
+        - "MIT"
       identifier: biotools:annosine
-
 input:
   - - meta:
         type: map
@@ -27,7 +26,7 @@ input:
         description: Input genome assembly
         pattern: "*.{fasta,fa,fsa}"
         ontologies:
-          - edam: http://edamontology.org/format_1929 # FASTA
+          - edam: http://edamontology.org/format_1929  #FASTA
   - mode:
       type: integer
       description: |
@@ -59,13 +58,27 @@ output:
           description: |
             Non-redundant SINE library with serial number
           pattern: "*.{fa}"
+  versions_annosine:
+    - - "${task.process}":
+          type: string
+          description: The name of the process
+      - "annosine":
+          type: string
+          description: The name of the tool
+      - 'pip show annosine2 | grep "^Version" | sed "s/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
+      - "annosine":
+          type: string
+          description: The name of the tool
+      - 'pip show annosine2 | grep "^Version" | sed "s/Version: //"':
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@GallVp"
 maintainers:

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

@@ -30,7 +30,7 @@ nextflow_process {
                 { assert path(process.out.log[0][1]).text.contains('AnnoSINE COMPLETE!') },
                 { assert snapshot(
                     process.out.fa,
-                    process.out.versions,
+                    process.out.findAll { key, val -> key.startsWith('versions') },
                     ).match()
                 }
             )

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

@@ -10,15 +10,21 @@
                     "test_annosine.fa:md5,fc3bd39555133a1b50623bccc7d4cf9b"
                 ]
             ],
-            [
-                "versions.yml:md5,b07e03bcf541df634bf5c47cbad4bd2f"
-            ]
+            {
+                "versions_annosine": [
+                    [
+                        "ANNOSINE",
+                        "annosine",
+                        "2.0.8"
+                    ]
+                ]
+            }
         ],
+        "timestamp": "2026-03-13T09:45:27.322794252",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
-        },
-        "timestamp": "2025-03-27T14:41:54.821745"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     },
     "actinidia_chinensis - fasta - stub": {
         "content": [
@@ -42,7 +48,11 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,b07e03bcf541df634bf5c47cbad4bd2f"
+                    [
+                        "ANNOSINE",
+                        "annosine",
+                        "2.0.8"
+                    ]
                 ],
                 "fa": [
                     [
@@ -62,15 +72,19 @@
                         "test_annosine.log:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,b07e03bcf541df634bf5c47cbad4bd2f"
+                "versions_annosine": [
+                    [
+                        "ANNOSINE",
+                        "annosine",
+                        "2.0.8"
+                    ]
                 ]
             }
         ],
+        "timestamp": "2026-03-13T09:46:04.662034254",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
-        },
-        "timestamp": "2025-03-27T14:40:02.826271"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     }
 }