Update to topics hamronization/*

modules/nf-core/hamronization/abricate/main.nf

@@ -16,7 +16,7 @@ process HAMRONIZATION_ABRICATE {
     output:
     tuple val(meta), path("*.json"), optional: true, emit: json
     tuple val(meta), path("*.tsv"), optional: true, emit: tsv
-    path "versions.yml", emit: versions
+    tuple val("${task.process}"), val('hamronization'), eval("hamronize --version 2>&1 | sed 's/hamronize //'"), topic: versions, emit: versions_hamronization
 
     when:
     task.ext.when == null || task.ext.when
@@ -33,21 +33,11 @@ process HAMRONIZATION_ABRICATE {
         --analysis_software_version ${software_version} \\
         --reference_database_version ${reference_db_version} \\
         > ${prefix}.${format}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        hamronization: \$(echo \$(hamronize --version 2>&1) | cut -f 2 -d ' ' )
-    END_VERSIONS
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.${format}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        hamronization: \$(echo \$(hamronize --version 2>&1) | cut -f 2 -d ' ' )
-    END_VERSIONS
     """
 }

modules/nf-core/hamronization/abricate/meta.yml

@@ -1,6 +1,6 @@
 name: "hamronization_abricate"
-description: Tool to convert and summarize ABRicate outputs using the hAMRonization
-  specification
+description: Tool to convert and summarize ABRicate outputs using the
+  hAMRonization specification
 keywords:
   - amr
   - antimicrobial resistance
@@ -13,14 +13,15 @@ tools:
       homepage: "https://github.com/pha4ge/hAMRonization/"
       documentation: "https://github.com/pha4ge/hAMRonization/"
       tool_dev_url: "https://github.com/pha4ge/hAMRonization"
-      licence: ["GNU Lesser General Public v3 (LGPL v3)"]
+      licence:
+        - "GNU Lesser General Public v3 (LGPL v3)"
       identifier: biotools:hamronization
 input:
   - - meta:
         type: map
         description: |
           Groovy Map containing sample information
-          e.g. [ id:'test', single_end:false ]
+          e.g. [ id:'test' ]
     - report:
         type: file
         description: Output TSV or CSV file from ABRicate
@@ -46,7 +47,7 @@ output:
           type: map
           description: |
             Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
+            e.g. [ id:'test' ]
       - "*.json":
           type: file
           description: hAMRonised report in JSON format
@@ -58,20 +59,34 @@ output:
           type: map
           description: |
             Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
+            e.g. [ id:'test' ]
       - "*.tsv":
           type: file
           description: hAMRonised report in TSV format
           pattern: "*.json"
           ontologies:
             - edam: http://edamontology.org/format_3464 # JSON
+  versions_hamronization:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - hamronization:
+          type: string
+          description: The name of the tool
+      - hamronize --version 2>&1 | sed 's/hamronize //':
+          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
+      - hamronization:
+          type: string
+          description: The name of the tool
+      - hamronize --version 2>&1 | sed 's/hamronize //':
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@jasmezz"
 maintainers:

modules/nf-core/hamronization/abricate/tests/main.nf.test

@@ -14,7 +14,10 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = [ [ id:"test" ], file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/hamronization/genome.abricate.tsv', checkIfExists: true) ]
+                input[0] = [
+                    [ id:"test" ],
+                    file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/hamronization/genome.abricate.tsv', checkIfExists: true)
+                ]
                 input[1] = 'tsv'
                 input[2] = '1.0.1'
                 input[3] = '2021-Mar-27'
@@ -25,7 +28,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
     }
@@ -37,7 +40,10 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = [ [ id:"test" ], file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/hamronization/genome.abricate.tsv', checkIfExists: true) ]
+                input[0] = [
+                    [ id:"test" ],
+                    file(params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/hamronization/genome.abricate.tsv', checkIfExists: true)
+                ]
                 input[1] = 'tsv'
                 input[2] = '1.0.1'
                 input[3] = '2021-Mar-27'
@@ -48,7 +54,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
     }

modules/nf-core/hamronization/abricate/tests/main.nf.test.snap

@@ -2,20 +2,6 @@
     "hamronization/abricate - bacteroides_fragilis - genome_abricate_tsv": {
         "content": [
             {
-                "0": [
-
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.tsv:md5,4b1024ba25c116a5312944f65dd40e9b"
-                    ]
-                ],
-                "2": [
-                    "versions.yml:md5,113fee72fb15d06692b7fc29ee477aff"
-                ],
                 "json": [
 
                 ],
@@ -27,34 +13,24 @@
                         "test.tsv:md5,4b1024ba25c116a5312944f65dd40e9b"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,113fee72fb15d06692b7fc29ee477aff"
+                "versions_hamronization": [
+                    [
+                        "HAMRONIZATION_ABRICATE",
+                        "hamronization",
+                        "1.1.9"
+                    ]
                 ]
             }
         ],
+        "timestamp": "2026-05-12T19:02:34.937482681",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.7"
-        },
-        "timestamp": "2025-10-04T06:44:38.664437882"
+            "nf-test": "0.9.4",
+            "nextflow": "26.03.0"
+        }
     },
     "hamronization/abricate - bacteroides_fragilis - genome_abricate_tsv - stub": {
         "content": [
             {
-                "0": [
-
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "2": [
-                    "versions.yml:md5,113fee72fb15d06692b7fc29ee477aff"
-                ],
                 "json": [
 
                 ],
@@ -66,15 +42,19 @@
                         "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,113fee72fb15d06692b7fc29ee477aff"
+                "versions_hamronization": [
+                    [
+                        "HAMRONIZATION_ABRICATE",
+                        "hamronization",
+                        "1.1.9"
+                    ]
                 ]
             }
         ],
+        "timestamp": "2026-05-12T19:02:41.628540543",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.7"
-        },
-        "timestamp": "2025-10-04T06:44:45.131612041"
+            "nf-test": "0.9.4",
+            "nextflow": "26.03.0"
+        }
     }
 }

modules/nf-core/hamronization/amrfinderplus/main.nf

@@ -16,7 +16,7 @@ process HAMRONIZATION_AMRFINDERPLUS {
     output:
     tuple val(meta), path("*.json"), optional: true, emit: json
     tuple val(meta), path("*.tsv"), optional: true, emit: tsv
-    path "versions.yml", emit: versions
+    tuple val("${task.process}"), val('hamronization'), eval("hamronize --version 2>&1 | sed 's/hamronize //'"), topic: versions, emit: versions_hamronization
 
     when:
     task.ext.when == null || task.ext.when
@@ -34,21 +34,11 @@ process HAMRONIZATION_AMRFINDERPLUS {
         --reference_database_version ${reference_db_version} \\
         --input_file_name ${prefix} \\
         > ${prefix}.${format}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        hamronization: \$(echo \$(hamronize --version 2>&1) | cut -f 2 -d ' ' )
-    END_VERSIONS
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.${format}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        hamronization: \$(echo \$(hamronize --version 2>&1) | cut -f 2 -d ' ' )
-    END_VERSIONS
     """
 }

modules/nf-core/hamronization/amrfinderplus/meta.yml

@@ -1,6 +1,6 @@
 name: "hamronization_amrfinderplus"
-description: Tool to convert and summarize AMRfinderPlus outputs using the hAMRonization
-  specification.
+description: Tool to convert and summarize AMRfinderPlus outputs using the
+  hAMRonization specification.
 keywords:
   - amr
   - antimicrobial resistance
@@ -15,20 +15,21 @@ tools:
       homepage: "https://github.com/pha4ge/hAMRonization/"
       documentation: "https://github.com/pha4ge/hAMRonization/"
       tool_dev_url: "https://github.com/pha4ge/hAMRonization"
-      licence: ["GNU Lesser General Public v3 (LGPL v3)"]
+      licence:
+        - "GNU Lesser General Public v3 (LGPL v3)"
       identifier: biotools:hamronization
 input:
   - - meta:
         type: map
         description: |
           Groovy Map containing sample information
-          e.g. [ id:'test', single_end:false ]
+          e.g. [ id:'test' ]
     - report:
         type: file
         description: Output .tsv file from AMRfinderPlus
         pattern: "*.tsv"
         ontologies:
-          - edam: http://edamontology.org/format_3475 # TSV
+          - edam: http://edamontology.org/format_3475
   - format:
       type: string
       description: Type of report file to be produced
@@ -47,7 +48,7 @@ output:
           type: map
           description: |
             Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
+            e.g. [ id:'test' ]
       - "*.json":
           type: file
           description: hAMRonised report in JSON format
@@ -59,20 +60,34 @@ output:
           type: map
           description: |
             Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
+            e.g. [ id:'test' ]
       - "*.tsv":
           type: file
           description: hAMRonised report in TSV format
           pattern: "*.tsv"
           ontologies:
             - edam: http://edamontology.org/format_3475 # TSV
+  versions_hamronization:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - hamronization:
+          type: string
+          description: The name of the tool
+      - hamronize --version 2>&1 | sed 's/hamronize //':
+          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
+      - hamronization:
+          type: string
+          description: The name of the tool
+      - hamronize --version 2>&1 | sed 's/hamronize //':
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@louperelo"
 maintainers: