migrate lissero module to topic channels

Author: Anifowak

modules/nf-core/lissero/environment.yml

@@ -5,3 +5,4 @@ channels:
   - bioconda
 dependencies:
   - bioconda::lissero=0.4.9
+  - setuptools=80.9.0

modules/nf-core/lissero/main.nf

@@ -12,7 +12,7 @@ process LISSERO {
 
     output:
     tuple val(meta), path("*.tsv"), emit: tsv
-    path "versions.yml"           , emit: versions
+    tuple val("${task.process}"), val('lissero'), val('0.4.9'), emit: versions_lissero, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -25,21 +25,11 @@ process LISSERO {
         $args \\
         $fasta \\
         > ${prefix}.tsv
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        lissero: \$( echo \$(lissero --version 2>&1) | sed 's/^.*LisSero //' )
-    END_VERSIONS
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.tsv
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        lissero: \$( echo \$(lissero --version 2>&1) | sed 's/^.*LisSero //' )
-    END_VERSIONS
     """
 }

modules/nf-core/lissero/meta.yml

@@ -10,7 +10,8 @@ tools:
       homepage: https://github.com/MDU-PHL/LisSero/blob/master/README.md
       documentation: https://github.com/MDU-PHL/LisSero/blob/master/README.md
       tool_dev_url: https://github.com/MDU-PHL/lissero
-      licence: ["GPL v3"]
+      licence:
+        - "GPL v3"
       identifier: ""
 input:
   - - meta:
@@ -35,14 +36,28 @@ output:
           description: Tab-delimited result file
           pattern: "*.tsv"
           ontologies:
-            - edam: http://edamontology.org/format_3475 # TSV
+            - edam: http://edamontology.org/format_3475
+  versions_lissero:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - lissero:
+          type: string
+          description: The name of the tool
+      - 0.4.9:
+          type: string
+          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
+      - lissero:
+          type: string
+          description: The name of the tool
+      - 0.4.9:
+          type: string
+          description: The expression to obtain the version of the tool
 authors:
   - "@rpetit3"
 maintainers:

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

@@ -24,10 +24,11 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(
-                    file(process.out.tsv[0][1]).readLines()[0], // Two line file. Line 2 contains a path.
-                    process.out.versions
-                    ).match()
+                {
+                  assert snapshot(
+                      file(process.out.tsv[0][1]).readLines()[0],
+                      sanitizeOutput(process.out, unstableKeys: ["tsv"])
+                  ).match()
                 }
             )
         }
@@ -55,3 +56,5 @@ nextflow_process {
     }
 
 }
+
+

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

@@ -3,7 +3,11 @@
         "content": [
             "ID\tSEROTYPE\tPRS\tLMO0737\tLMO1118\tORF2110\tORF2819\tCOMMENT",
             [
-                "versions.yml:md5,f091db71715241a5f46beacaf97dc08b"
+                  [
+                      "LISSERO",
+                      "lissero",
+                      "0.4.9"
+                   ]
             ]
         ],
         "meta": {
@@ -25,7 +29,11 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,f091db71715241a5f46beacaf97dc08b"
+                    [
+                      "LISSERO",
+                      "lissero",
+                      "0.4.9"
+                   ]
                 ],
                 "tsv": [
                     [
@@ -36,8 +44,12 @@
                         "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,f091db71715241a5f46beacaf97dc08b"
+                "versions_lissero": [
+                    [
+                      "LISSERO",
+                      "lissero",
+                      "0.4.9"
+                   ]
                 ]
             }
         ],
@@ -47,4 +59,6 @@
         },
         "timestamp": "2024-08-30T15:08:59.133959"
     }
-}
+}
+
+