Update smoothxg: topic versions, stub block, sanitizeOutput

modules/nf-core/smoothxg/main.nf

@@ -13,7 +13,7 @@ process SMOOTHXG {
     output:
     tuple val(meta), path("*smoothxg.gfa"), emit: gfa
     path("*.maf") , optional: true, emit: maf
-    path "versions.yml"           , emit: versions
+    tuple val("${task.process}"), val('smoothxg'), eval("smoothxg --version 2>&1 | sed 's/^v//; s/-.*//'"), topic: versions, emit: versions_smoothxg
 
     when:
     task.ext.when == null || task.ext.when
@@ -27,10 +27,11 @@ process SMOOTHXG {
         --gfa-in=${gfa} \\
         --smoothed-out=${prefix}.smoothxg.gfa \\
         $args
+    """
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        smoothxg: \$(smoothxg --version 2>&1 | cut -f 1 -d '-' | cut -f 2 -d 'v')
-    END_VERSIONS
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.smoothxg.gfa
     """
 }

modules/nf-core/smoothxg/meta.yml

@@ -1,6 +1,6 @@
 name: smoothxg
-description: Linearize and simplify variation graph in GFA format using blocked partial
-  order alignment
+description: Linearize and simplify variation graph in GFA format using blocked
+  partial order alignment
 keywords:
   - gfa
   - graph
@@ -14,7 +14,8 @@ tools:
         order alignment.
       homepage: https://github.com/pangenome/smoothxg
       documentation: https://github.com/pangenome/smoothxg
-      licence: ["MIT"]
+      licence:
+        - "MIT"
       identifier: ""
 input:
   - - meta:
@@ -44,17 +45,31 @@ output:
   maf:
     - "*.maf":
         type: file
-        description: write the multiple sequence alignments (MSAs) in MAF format in
-          this file (optional)
+        description: write the multiple sequence alignments (MSAs) in MAF format
+          in this file (optional)
         pattern: "*.{maf}"
         ontologies: []
+  versions_smoothxg:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - smoothxg:
+          type: string
+          description: The name of the tool
+      - "smoothxg --version 2>&1 | sed 's/^v//; s/-.*//'":
+          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
+      - smoothxg:
+          type: string
+          description: The name of the tool
+      - "smoothxg --version 2>&1 | sed 's/^v//; s/-.*//'":
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@heuermh, @subwaystation"
 maintainers:

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

@@ -25,7 +25,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-//                 { assert snapshot(process.out).match() } // SMOOTHXG is never deterministic
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
 
@@ -47,7 +47,31 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-//                 { assert snapshot(process.out).match() } // SMOOTHXG is never deterministic
+                { assert snapshot(sanitizeOutput(process.out)).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - illumina - assembly_gfa - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/gfa/assembly.gfa', checkIfExists: true)
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
 

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

@@ -2,38 +2,91 @@
     "sarscov2 - illumina - assembly_gfa": {
         "content": [
             {
-                "0": [
+                "gfa": [
                     [
                         {
                             "id": "test",
                             "single_end": false
                         },
-                        "test.smoothxg.gfa:md5,c85140490fb255f8361499c01d0dd15b"
+                        "test.smoothxg.gfa:md5,f0991ef0f6a54dcbae0454c812256664"
                     ]
                 ],
-                "1": [
+                "maf": [
                     "test.maf:md5,a6d82f572a5358926b87c69683d7825e"
                 ],
-                "2": [
-                    "versions.yml:md5,14c3d1a28b189a6db45facabbb5dc274"
+                "versions_smoothxg": [
+                    [
+                        "SMOOTHXG",
+                        "smoothxg",
+                        "0.8.0"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-04-30T17:40:45.061861",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
+    },
+    "sarscov2 - illumina - assembly_gfa - stub": {
+        "content": [
+            {
+                "gfa": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.smoothxg.gfa:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "maf": [
+
                 ],
+                "versions_smoothxg": [
+                    [
+                        "SMOOTHXG",
+                        "smoothxg",
+                        "0.8.0"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-04-30T17:41:00.367248",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
+    },
+    "homo_sapiens - pangenome - pangenome_seqwish_gfa": {
+        "content": [
+            {
                 "gfa": [
                     [
                         {
                             "id": "test",
                             "single_end": false
                         },
-                        "test.smoothxg.gfa:md5,c85140490fb255f8361499c01d0dd15b"
+                        "test.smoothxg.gfa:md5,4a3d6a9bcb0bb5dcf10a9ff41fc900e7"
                     ]
                 ],
                 "maf": [
-                    "test.maf:md5,a6d82f572a5358926b87c69683d7825e"
+                    "test.maf:md5,f974a7502bcf6eb59574832694664df9"
                 ],
-                "versions": [
-                    "versions.yml:md5,14c3d1a28b189a6db45facabbb5dc274"
+                "versions_smoothxg": [
+                    [
+                        "SMOOTHXG",
+                        "smoothxg",
+                        "0.8.0"
+                    ]
                 ]
             }
         ],
-        "timestamp": "2024-01-25T16:06:35.857843316"
+        "timestamp": "2026-04-30T17:40:55.500873",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     }
 }