Update to topics hmtnote

modules/nf-core/hmtnote/annotate/main.nf

@@ -12,34 +12,42 @@ process HMTNOTE_ANNOTATE {
 
     output:
     tuple val(meta), path("*_annotated.vcf"), emit: vcf
-    path "versions.yml"           , emit: versions
+    tuple val("${task.process}"), val('hmtnote'), eval("hmtnote --version 2>&1 | sed 's/.*version //'"), emit: versions_hmtnote, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
+    def deprecation_message = """
+WARNING: This module has been deprecated.
+
+Reason:
+This tool is no longer maintained by its author and, as its database hosting service has
+been discontinued, it can no longer work with conda.
+"""
+    assert false: deprecation_message
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
 
     """
     hmtnote \\
         annotate \\
-        $vcf \\
+        ${vcf} \\
         ${prefix}_annotated.vcf \\
-        $args
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        hmtnote: \$(echo \$(hmtnote --version 2>&1) | sed 's/^.*hmtnote, version //; s/Using.*\$//' ))
-    END_VERSIONS
+        ${args}
     """
+
     stub:
+        def deprecation_message = """
+WARNING: This module has been deprecated.
+
+Reason:
+This tool is no longer maintained by its author and, as its database hosting service has
+been discontinued, it can no longer work with conda.
+"""
+    assert false: deprecation_message
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}_annotated.vcf
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        hmtnote: \$(echo \$(hmtnote --version 2>&1) | sed 's/^.*hmtnote, version //; s/Using.*\$//' ))
-    END_VERSIONS
     """
 }

modules/nf-core/hmtnote/annotate/meta.yml

@@ -1,6 +1,7 @@
 name: hmtnote_annotate
-description: Human mitochondrial variants annotation using HmtVar. Contains .plk file
-  with annotation, so can be run offline
+description: Human mitochondrial variants annotation using HmtVar. Contains .plk
+  file with annotation, so can be run offline
+deprecated: true
 keywords:
   - hmtnote
   - mitochondria
@@ -11,7 +12,8 @@ tools:
       homepage: https://github.com/robertopreste/HmtNote
       documentation: https://hmtnote.readthedocs.io/en/latest/usage.html
       doi: "10.1101/600619"
-      licence: ["MIT"]
+      licence:
+        - "MIT"
       identifier: ""
 input:
   - - meta:
@@ -34,13 +36,27 @@ output:
           description: annotated vcf
           pattern: "*_annotated.vcf"
           ontologies: []
+  versions_hmtnote:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - hmtnote:
+          type: string
+          description: The name of the tool
+      - hmtnote --version 2>&1 | 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
+      - hmtnote:
+          type: string
+          description: The name of the tool
+      - hmtnote --version 2>&1 | sed 's/.*version //':
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@sysbiocoder"
 maintainers:

modules/nf-core/hmtnote/annotate/tests/main.nf.test

@@ -23,19 +23,19 @@ nextflow_process {
                     [ id:'test' ],
 				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true)
 				]
-
                 """
             }
         }
 
         then {
             assertAll(
-                { assert process.success },
+                { assert process.failed },
+                { assert process.errorReport.contains("WARNING: This module has been deprecated.")}
+                /*{ assert process.success },
                 { assert snapshot(
 					path(process.out.vcf[0][1]).vcf.variantsMD5,
-					process.out.versions
-					).match()
-				}
+					process.out.findAll { key, val -> key.startsWith('versions') }
+                ).match()}*/
             )
         }
     }
@@ -52,15 +52,16 @@ nextflow_process {
                     [ id:'test' ],
 				    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true)
 				]
-
                 """
             }
         }
 
         then {
             assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert process.failed },
+                { assert process.errorReport.contains("WARNING: This module has been deprecated.")}
+                /*{ assert process.success },
+                { assert snapshot(sanitizeOutput(process.out)).match() }*/
             )
         }
     }

modules/nf-core/hmtnote/annotate/tests/main.nf.test.snap

@@ -2,47 +2,46 @@
     "sarscov2 - stub": {
         "content": [
             {
-                "0": [
+                "vcf": [
                     [
                         {
                             "id": "test"
                         },
                         "test_annotated.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "1": [
-                    "versions.yml:md5,8ee58af72515ea6d362a7721c3ba1340"
-                ],
-                "vcf": [
+                "versions_hmtnote": [
                     [
-                        {
-                            "id": "test"
-                        },
-                        "test_annotated.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "HMTNOTE_ANNOTATE",
+                        "hmtnote",
+                        "0.7.2"
                     ]
-                ],
-                "versions": [
-                    "versions.yml:md5,8ee58af72515ea6d362a7721c3ba1340"
                 ]
             }
         ],
+        "timestamp": "2026-05-19T17:52:47.633542465",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.2"
-        },
-        "timestamp": "2025-05-15T13:43:56.953856721"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     },
     "sarscov2": {
         "content": [
             "98d1056442ec88659f26dfb1251b6f74",
-            [
-                "versions.yml:md5,8ee58af72515ea6d362a7721c3ba1340"
-            ]
+            {
+                "versions_hmtnote": [
+                    [
+                        "HMTNOTE_ANNOTATE",
+                        "hmtnote",
+                        "0.7.2"
+                    ]
+                ]
+            }
         ],
+        "timestamp": "2026-05-19T17:52:32.708662033",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.2"
-        },
-        "timestamp": "2025-05-15T13:43:44.674273215"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     }
 }

modules/nf-core/hmtnote/annotate/tests/nextflow.config

@@ -1,5 +1,5 @@
 process {
     withName: HMTNOTE_ANNOTATE {
-        ext.args =params.module_args
+        ext.args = params.module_args
     }
 }