migrate leviosam2/lift module to topic channels

Author: Anifowak

modules/nf-core/leviosam2/lift/main.nf

@@ -9,11 +9,11 @@ process LEVIOSAM2_LIFT {
 
     input:
     tuple val(meta), path(input)
-    tuple val(meta_ref), path(clft)
+    tuple val(meta2), path(clft)
 
     output:
     tuple val(meta), path("*.bam"), emit: bam
-    path "versions.yml"           , emit: versions
+    tuple val("${task.process}"), val('leviosam2'), eval("leviosam2 --version"), emit: versions_leviosam2, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -30,21 +30,11 @@ process LEVIOSAM2_LIFT {
         -p ${prefix} \\
         -O bam \\
         ${args}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        leviosam2: \$(leviosam2 --version)
-    END_VERSIONS
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.bam
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        leviosam2: \$(leviosam2 --version)
-    END_VERSIONS
     """
 }

modules/nf-core/leviosam2/lift/meta.yml

@@ -1,6 +1,6 @@
 name: "leviosam2_lift"
-description: Converting aligned short and long reads records from one reference to
-  another
+description: Converting aligned short and long reads records from one reference
+  to another
 keywords:
   - leviosam2
   - index
@@ -10,7 +10,8 @@ tools:
       description: "Fast and accurate coordinate conversion between assemblies"
       homepage: "https://github.com/milkschen/leviosam2/blob/main/workflow/README.md"
       documentation: "https://github.com/milkschen/leviosam2/blob/main/workflow/README.md"
-      licence: ["MIT"]
+      licence:
+        - "MIT"
       identifier: ""
 input:
   - - meta:
@@ -23,7 +24,7 @@ input:
         description: SAM/BAM/CRAM file to be lifted
         pattern: "*.{bam}"
         ontologies: []
-  - - meta_ref:
+  - - meta2:
         type: map
         description: |
           Groovy Map containing reference information
@@ -45,13 +46,27 @@ output:
           description: Lifted bam file
           pattern: "*.{bam}"
           ontologies: []
+  versions_leviosam2:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - "leviosam2":
+          type: string
+          description: The name of the tool
+      - leviosam2 --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
+      - "leviosam2":
+          type: string
+          description: The name of the tool
+      - leviosam2 --version:
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@lgrochowalski"
 maintainers:

modules/nf-core/leviosam2/lift/tests/main.nf.test

@@ -58,7 +58,7 @@ nextflow_process {
                 {
                     assert snapshot(
                         process.out.bam.collect { file(it[1]).getName() },
-                        process.out.versions
+                        process.out.findAll { key, val -> key.startsWith('versions') },
                     ).match()
                 }
             )
@@ -113,7 +113,7 @@ nextflow_process {
                 {
                     assert snapshot(
                         process.out.bam.collect { file(it[1]).getName() },
-                        process.out.versions
+                        process.out.findAll { key, val -> key.startsWith('versions') },
                     ).match()
                 }
             )
@@ -143,10 +143,13 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(sanitizeOutput(process.out)).match()
+                }
             )
         }
 
     }
 
 }
+
+

modules/nf-core/leviosam2/lift/tests/main.nf.test.snap

@@ -5,7 +5,11 @@
                 "test.bam"
             ],
             [
-                "versions.yml:md5,331d0fec62acbb6e8366e836e7e15469"
+                [
+                    "LEVIOSAM2_LIFT",
+                    "leviosam2",
+                    "0.4.2"
+                ]
             ]
         ],
         "meta": {
@@ -27,7 +31,11 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,331d0fec62acbb6e8366e836e7e15469"
+                    [
+                        "LEVIOSAM2_LIFT",
+                        "leviosam2",
+                        "0.4.2"
+                    ]
                 ],
                 "bam": [
                     [
@@ -38,10 +46,14 @@
                         "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,331d0fec62acbb6e8366e836e7e15469"
+                "versions_leviosam2": [
+                    [
+                        "LEVIOSAM2_LIFT",
+                        "leviosam2",
+                        "0.4.2"
+                    ]
                 ]
-            }
+             }
         ],
         "meta": {
             "nf-test": "0.8.4",
@@ -55,7 +67,11 @@
                 "test.bam"
             ],
             [
-                "versions.yml:md5,331d0fec62acbb6e8366e836e7e15469"
+                [
+                    "LEVIOSAM2_LIFT",
+                    "leviosam2",
+                    "0.4.2"
+                ]
             ]
         ],
         "meta": {
@@ -64,4 +80,5 @@
         },
         "timestamp": "2024-06-25T12:18:17.99171"
     }
-}
+}
+