Xengsort to topics

Author: SPPearce

modules/nf-core/xengsort/index/main.nf

@@ -17,7 +17,7 @@ process XENGSORT_INDEX {
     output:
     path "${index}.hash"          , emit: hash
     path "${index}.info"          , emit: info
-    path "versions.yml"           , emit: versions
+    tuple val("${task.process}"), val('xengsort'), eval("xengsort --version"), topic: versions, emit: versions_xengsort
 
     when:
     task.ext.when == null || task.ext.when
@@ -33,21 +33,11 @@ process XENGSORT_INDEX {
         --graft $graft_fasta \\
         --nobjects $nobjects \\
         --mask '$mask' \\
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        xengsort: \$(xengsort --version)
-    END_VERSIONS
     """
 
     stub:
     """
     touch ${index}.info
     touch ${index}.hash
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        xengsort: \$(xengsort --version)
-    END_VERSIONS
     """
 }

modules/nf-core/xengsort/index/meta.yml

@@ -16,9 +16,9 @@ tools:
       documentation: "https://gitlab.com/genomeinformatics/xengsort"
       tool_dev_url: "https://gitlab.com/genomeinformatics/xengsort"
       doi: "10.4230/LIPIcs.WABI.2020.4"
-      licence: ["MIT"]
+      licence:
+        - "MIT"
       identifier: ""
-
 input:
   - host_fasta:
       type: file
@@ -55,13 +55,27 @@ output:
         description: File with index info file.
         pattern: "*info"
         ontologies: []
+  versions_xengsort:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - xengsort:
+          type: string
+          description: The name of the tool
+      - xengsort --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
+      - xengsort:
+          type: string
+          description: The name of the tool
+      - xengsort --version:
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@diegomscoelho"
 maintainers:

modules/nf-core/xengsort/index/tests/main.nf.test

@@ -28,7 +28,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
 

modules/nf-core/xengsort/index/tests/main.nf.test.snap

@@ -2,30 +2,25 @@
     "homo_sapiens - sarscov2 - stub": {
         "content": [
             {
-                "0": [
-                    "index.hash:md5,d41d8cd98f00b204e9800998ecf8427e"
-                ],
-                "1": [
-                    "index.info:md5,d41d8cd98f00b204e9800998ecf8427e"
-                ],
-                "2": [
-                    "versions.yml:md5,ede2e0a7a166d5af516a5c15ff6891d5"
-                ],
                 "hash": [
                     "index.hash:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ],
                 "info": [
                     "index.info:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ],
-                "versions": [
-                    "versions.yml:md5,ede2e0a7a166d5af516a5c15ff6891d5"
+                "versions_xengsort": [
+                    [
+                        "XENGSORT_INDEX",
+                        "xengsort",
+                        "2.0.5"
+                    ]
                 ]
             }
         ],
+        "timestamp": "2026-06-16T11:32:20.570762076",
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-03-28T13:35:44.83309745"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     }
 }