From 0e01ffe99a28c75424f7405749a11c5533e27e66 Mon Sep 17 00:00:00 2001
From: "Harrison H. Vaughn Reed" <harrisonhvreed@gmail.com>
Date: Thu, 30 Apr 2026 17:37:06 -0400
Subject: [PATCH 1/3] feat(wfmash): migrate to topic: versions, add stub block,
 sanitizeOutput assertions

---
 modules/nf-core/wfmash/main.nf                | 12 ++--
 modules/nf-core/wfmash/meta.yml               | 40 +++++++++----
 modules/nf-core/wfmash/tests/main.nf.test     | 31 +++++++++-
 .../nf-core/wfmash/tests/main.nf.test.snap    | 58 ++++++++++++++++---
 4 files changed, 114 insertions(+), 27 deletions(-)

diff --git a/modules/nf-core/wfmash/main.nf b/modules/nf-core/wfmash/main.nf
index 4cb9b7ac7c94..d3d3534a0bdf 100644
--- a/modules/nf-core/wfmash/main.nf
+++ b/modules/nf-core/wfmash/main.nf
@@ -14,7 +14,7 @@ process WFMASH {
 
     output:
     tuple val(meta), path("*.paf"), emit: paf
-    path "versions.yml"           , emit: versions
+    tuple val("${task.process}"), val('wfmash'), eval('echo $(wfmash --version 2>&1) | cut -f 1 -d \'-\' | cut -f 2 -d \'v\''), topic: versions, emit: versions_wfmash
 
 
     when:
@@ -34,11 +34,11 @@ process WFMASH {
         --threads $task.cpus \\
         $paf_mappings \\
         $args > ${prefix}.paf
+    """
 
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        wfmash: \$(echo \$(wfmash --version 2>&1) | cut -f 1 -d '-' | cut -f 2 -d 'v')
-    END_VERSIONS
+    stub:
+    def prefix = task.ext.prefix ? task.ext.prefix : paf ? "${meta.id}" + "." + paf.baseName.split("\\.")[-1] : "${meta.id}"
+    """
+    touch ${prefix}.paf
     """
 }
diff --git a/modules/nf-core/wfmash/meta.yml b/modules/nf-core/wfmash/meta.yml
index 5f74547feca8..e0423f913e0d 100644
--- a/modules/nf-core/wfmash/meta.yml
+++ b/modules/nf-core/wfmash/meta.yml
@@ -13,7 +13,8 @@ tools:
       documentation: https://github.com/waveygang/wfmash
       tool_dev_url: https://github.com/waveygang/wfmash
       doi: 10.5281/zenodo.6949373
-      licence: ["MIT"]
+      licence:
+        - "MIT"
       identifier: ""
 input:
   - - meta:
@@ -28,8 +29,8 @@ input:
         ontologies: []
     - paf:
         type: file
-        description: Optional inpute file in PAF format to derive the precise alignments
-          for.
+        description: Optional inpute file in PAF format to derive the precise
+          alignments for.
         pattern: "*.{paf}"
         ontologies: []
     - gzi:
@@ -44,11 +45,12 @@ input:
         ontologies: []
   - query_self:
       type: boolean
-      description: If set to true, the input FASTA will also be used as the query FASTA.
+      description: If set to true, the input FASTA will also be used as the query
+        FASTA.
   - fasta_query_list:
       type: file
-      description: Optional inpute file in FASTA format specifying the query sequences
-        as a list.
+      description: Optional inpute file in FASTA format specifying the query
+        sequences as a list.
       pattern: "*.{fa,fna,fasta}"
       ontologies: []
 output:
@@ -63,13 +65,27 @@ output:
           description: Alignments in PAF format
           pattern: "*.{paf}"
           ontologies: []
+  versions_wfmash:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - wfmash:
+          type: string
+          description: The name of the tool
+      - echo $(wfmash --version 2>&1) | cut -f 1 -d '-' | cut -f 2 -d 'v':
+          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
+      - wfmash:
+          type: string
+          description: The name of the tool
+      - echo $(wfmash --version 2>&1) | cut -f 1 -d '-' | cut -f 2 -d 'v':
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@subwaystation"
 maintainers:
diff --git a/modules/nf-core/wfmash/tests/main.nf.test b/modules/nf-core/wfmash/tests/main.nf.test
index 721541dd5589..24147fee030a 100644
--- a/modules/nf-core/wfmash/tests/main.nf.test
+++ b/modules/nf-core/wfmash/tests/main.nf.test
@@ -30,7 +30,36 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.versions).match("versions") }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - pangenome - pangenome_fa_bgzip - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'pangenomics/homo_sapiens/pangenome.fa.gz', checkIfExists: true),
+                    [], // empty paf input
+                    file(params.modules_testdata_base_path + 'pangenomics/homo_sapiens/pangenome.fa.gz.gzi', checkIfExists: true), // gzi
+                    file(params.modules_testdata_base_path + 'pangenomics/homo_sapiens/pangenome.fa.gz.fai', checkIfExists: true) // fai
+                ]
+                input[1] = true // empty paf input
+                input[2] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
 
diff --git a/modules/nf-core/wfmash/tests/main.nf.test.snap b/modules/nf-core/wfmash/tests/main.nf.test.snap
index aa1116279821..204355aafa70 100644
--- a/modules/nf-core/wfmash/tests/main.nf.test.snap
+++ b/modules/nf-core/wfmash/tests/main.nf.test.snap
@@ -1,14 +1,56 @@
 {
-    "versions": {
+    "homo_sapiens - pangenome - pangenome_fa_bgzip - stub": {
         "content": [
-            [
-                "versions.yml:md5,9f9bd116e78512f26ddf28b51a46e64e"
-            ]
+            {
+                "paf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.paf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions_wfmash": [
+                    [
+                        "WFMASH",
+                        "wfmash",
+                        "0.13.0"
+                    ]
+                ]
+            }
         ],
+        "timestamp": "2026-04-30T17:43:11.682538",
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
-        },
-        "timestamp": "2024-04-11T15:02:01.736721962"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
+    },
+    "homo_sapiens - pangenome - pangenome_fa_bgzip": {
+        "content": [
+            {
+                "paf": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.paf:md5,180128cf59433692358b992ba4fdec30"
+                    ]
+                ],
+                "versions_wfmash": [
+                    [
+                        "WFMASH",
+                        "wfmash",
+                        "0.13.0"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-04-30T17:43:06.248425",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     }
 }
\ No newline at end of file

From d65ae3b83b0544adbb7313eabac995db9b409382 Mon Sep 17 00:00:00 2001
From: "Harrison H. Vaughn Reed" <harrisonhvreed@gmail.com>
Date: Fri, 1 May 2026 07:13:11 -0400
Subject: [PATCH 2/3] Standardize version emission and restore EDAM comments

---
 modules/nf-core/wfmash/main.nf  | 2 +-
 modules/nf-core/wfmash/meta.yml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/wfmash/main.nf b/modules/nf-core/wfmash/main.nf
index d3d3534a0bdf..09a734181885 100644
--- a/modules/nf-core/wfmash/main.nf
+++ b/modules/nf-core/wfmash/main.nf
@@ -14,7 +14,7 @@ process WFMASH {
 
     output:
     tuple val(meta), path("*.paf"), emit: paf
-    tuple val("${task.process}"), val('wfmash'), eval('echo $(wfmash --version 2>&1) | cut -f 1 -d \'-\' | cut -f 2 -d \'v\''), topic: versions, emit: versions_wfmash
+    tuple val("${task.process}"), val('wfmash'), eval('echo $(wfmash --version 2>&1) | cut -f 1 -d \'-\' | cut -f 2 -d \'v\''), topic: versions, emit: versions
 
 
     when:
diff --git a/modules/nf-core/wfmash/meta.yml b/modules/nf-core/wfmash/meta.yml
index e0423f913e0d..8c42e414e56a 100644
--- a/modules/nf-core/wfmash/meta.yml
+++ b/modules/nf-core/wfmash/meta.yml
@@ -65,7 +65,7 @@ output:
           description: Alignments in PAF format
           pattern: "*.{paf}"
           ontologies: []
-  versions_wfmash:
+  versions:
     - - ${task.process}:
           type: string
           description: The name of the process

From a9ef0a7ee19af79309137db1f7d9b786a4b3bf20 Mon Sep 17 00:00:00 2001
From: "Harrison H. Vaughn Reed" <harrisonhvreed@gmail.com>
Date: Fri, 1 May 2026 09:20:51 -0400
Subject: [PATCH 3/3] fix(wfmash): rename emit to versions_wfmash, simplify
 eval, update snapshots

- main.nf: emit: versions -> emit: versions_wfmash
- meta.yml: output key versions: -> versions_wfmash:
- main.nf/meta.yml: simplify eval string to use sed instead of dual cuts
- tests/main.nf.test.snap: regenerate snapshots

Local lint: 52/0. Local nf-test: 2/2 passed.
---
 modules/nf-core/wfmash/main.nf                 | 2 +-
 modules/nf-core/wfmash/meta.yml                | 6 +++---
 modules/nf-core/wfmash/tests/main.nf.test.snap | 4 ++--
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/modules/nf-core/wfmash/main.nf b/modules/nf-core/wfmash/main.nf
index 09a734181885..fbfca946f06c 100644
--- a/modules/nf-core/wfmash/main.nf
+++ b/modules/nf-core/wfmash/main.nf
@@ -14,7 +14,7 @@ process WFMASH {
 
     output:
     tuple val(meta), path("*.paf"), emit: paf
-    tuple val("${task.process}"), val('wfmash'), eval('echo $(wfmash --version 2>&1) | cut -f 1 -d \'-\' | cut -f 2 -d \'v\''), topic: versions, emit: versions
+    tuple val("${task.process}"), val('wfmash'), eval("wfmash --version 2>&1 | sed 's/^v//; s/-.*//'"), topic: versions, emit: versions_wfmash
 
 
     when:
diff --git a/modules/nf-core/wfmash/meta.yml b/modules/nf-core/wfmash/meta.yml
index 8c42e414e56a..accb16ee92c3 100644
--- a/modules/nf-core/wfmash/meta.yml
+++ b/modules/nf-core/wfmash/meta.yml
@@ -65,14 +65,14 @@ output:
           description: Alignments in PAF format
           pattern: "*.{paf}"
           ontologies: []
-  versions:
+  versions_wfmash:
     - - ${task.process}:
           type: string
           description: The name of the process
       - wfmash:
           type: string
           description: The name of the tool
-      - echo $(wfmash --version 2>&1) | cut -f 1 -d '-' | cut -f 2 -d 'v':
+      - "wfmash --version 2>&1 | sed 's/^v//; s/-.*//'":
           type: eval
           description: The expression to obtain the version of the tool
 topics:
@@ -83,7 +83,7 @@ topics:
       - wfmash:
           type: string
           description: The name of the tool
-      - echo $(wfmash --version 2>&1) | cut -f 1 -d '-' | cut -f 2 -d 'v':
+      - "wfmash --version 2>&1 | sed 's/^v//; s/-.*//'":
           type: eval
           description: The expression to obtain the version of the tool
 authors:
diff --git a/modules/nf-core/wfmash/tests/main.nf.test.snap b/modules/nf-core/wfmash/tests/main.nf.test.snap
index 204355aafa70..7f0d4f7c56a7 100644
--- a/modules/nf-core/wfmash/tests/main.nf.test.snap
+++ b/modules/nf-core/wfmash/tests/main.nf.test.snap
@@ -35,7 +35,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.paf:md5,180128cf59433692358b992ba4fdec30"
+                        "test.paf:md5,29f914ce85ab77a33bd740d1f9570eec"
                     ]
                 ],
                 "versions_wfmash": [
@@ -47,7 +47,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-04-30T17:43:06.248425",
+        "timestamp": "2026-05-01T09:19:21.270932",
         "meta": {
             "nf-test": "0.9.5",
             "nextflow": "26.04.0"